Skype: RAW Kenya

Coral Reef & Fish Monitoring

1. Introduction

The Kisite-Mpunguti Marine National Park is situated on Kenya’s south coast off Shimoni, lying just south of Wasini Island, near the Tanzanian border. The Kisite MPA covers approximately 11km2 while the Mpunguti marine reserve covers approximately 28km2. The marine park boasts incredible snorkelling and diving as well as being one of the most likely areas for spotting cetaceans. Therefore it is not surprising that this area
is a very popular tourist destination bringing in vital revenue for local businesses and people. Small, short term research/monitoring studies have been conducted on this marine park in the past, however, long term monitoring and management has not yet been established. This is vital for the protection and preservation of one of East Africa’s most pristine marine sites and the future of its local people.

2. Aims

The overall aim for this project is to create an extensive long-term monitoring programme within the Kisite- Mpunguti marine park which will be conducted to detect any changes to the health of the coral reefs and abundances of associated fish species and invertebrates.
In order to accomplish this, short term goals have to be completed prior. These are as follows:

  • Accurate mapping of both protected and unprotected coral reefs
  • Establish a current baseline health of the protected and unprotected reefs
  • Establish a current species list and abundances of associated reef fishes and invertebrates
  • Creating extensive long term fish abundances & size estimates data set to assess effectiveness of FAD’s

3. Basic Coral Morphology

Identifying corals to species level requires specialist knowledge, microscopes, and lots of time. For conservation, mapping, and monitoring purposes, you will only be required to be able to recognise different growth forms and be able to ID obvious species to genus level (commonly used in coral conservation practices).

3.1. Colony morphology (shapes)

The shapes of coral colonies usually depend on growth rates and modes of reproduction.

Colonies are commonly found as follows:

  • Massive – similar in all directions
  • Columnar – forms columns
  • Encrusting – sticking to the substrate
  • Branching – tree/finger like
  • Foliaceous – leaf like
  • Laminar – plate like
  • Free – Living

Coral Genre

3.2. Examples of commonly found coral genera


Acropora are by far the most common and fastest growing (averaging up to 10cm per year) coral genera. They are usually found in branching form. However they can also be found growing in a laminar form or forming bushy colonies.

Acropora are by far the most common and fastest growing (averaging up to 10cm per year) coral genera. They are usually found in branching form. However they can also be found growing in a laminar form or forming bushy colonies.


Pocillopora is also very common and is usually found as a clumped branching colony and are distinctive due to their ‘wart-like’ growths that cover the colony.


Porites can be flat, massive or branching in growth form. This genera is very common and can form massive structures (e.g. domed coral that can reach 8m in height). Corals of this genus grow extremely slowly (up to 10mm per year) therefore large species of this genus are usually several hundred years old.

Due to their slow growth rates this genus can become rare in some areas and take centuries to recover.


Coral diseases generally occur in response to biotic (living) stresses such as bacteria, fungi and viruses. However abiotic (non-living) factors such as increases in sea surface temperatures, UV radiation, sedimentation and toxic pollutants are also key players. Coral diseases have increased in frequency over the past few decades causing widespread mortality. It is now commonly accepted that this increase in coral disease is mostly related to poor water quality which allows the proliferation and colonisation of diseasecausing micro-organisms.

Black Band Disease (BBD)

Black band disease (BBD) is characterised by a blackish concentric band separating healthy and bleached coral tissue. It was first discorvered on the reefs of Belize and Florida in the early 1970’s and has since been discovered in over 26 countries. BBD is primarily caused by cyanobacteria, although other synergistic, photosynthetic and non-photosynthetic micro-organisms may also be responsible. The increase in BBD incidences have been linked to coral stress, such as increased sedimentation, eutrophication, and increased toxins into the water column.

Coral Bleaching

Climate change is a very serious threat to coral reefs with primary causes of death as a result of climate change being coral bleaching events. Due to elevated sea surface temperatures symbiotic algae, known as zooxanthellae, are lost from coral cells. Zooanthellae are crucial in coral survival, as they essentially ‘feed’ them. As a result of the symbiotic algal loss, the corals die and reveal a white skeleton (hence are termed to be ‘bleached’). The most severe bleaching event in the Indian Ocean ocurred in 1997-98 where 95% of corals were lost spanning a range of countries Kenya included. The primary cause was an average increase in sea surface temperature by just over 1oC above normal conditions for that time of year due to El Nino, incidentally the worst one on record to date.

Blackband Disease

Black Band Disease (left photo) & Coral Bleaching (right photo)

Monitoring of coral diseases is crucial due to the links with anthropogenic and natural phenomena. Detection of such diseases is crucial as mitigation measures can be made quickly in order to prevent further coral degredation.

4. Examples of Coral Associated Organisms

As there are thousands of different species of coral associated organisms on the reefs of East Africa, it would be impractical to name all of them, therefore just a few of the most likely species you will encounter are mentioned here. It is up to you to familiarise yourself with other species that may also present (see recommended reading)

Echinometra mathaei (burrowing urchin)

Echinometra mathaei (burrowing urchin)

E. mathaei, the burrowing urchin, is very common around the shallow waters of East Africa. The colours of this species of urchin varies greatly however this species is easily distinguished from other species by its characteristic pale ring at the base of each spine. Due to its burrowing activities it causes bioerosion of coral reefs, and due to its natural predators being primarily finfish (e.g. trigger fish), they are clear indicators of overfishing as a result of predator removal.

Chaetodontidae (Butterflyfish)

Chaetodontidae (Butterflyfish)

Butterflyfish (Family Chaetodontidae) come in a vast array of different, usually bright, colours. There are approximately 114 species in total and are extremely common on reefs around the world. What is common throughout all species of butterflyfish is their thin, disc shaped bodies that closely resembles their cousin species, angel fish. Many species also have dark bands across their eyes and round, eye like spots of their sides which is believed to confuse predators.

The habitat types will include coral reefs and seagrass beds with a possibility of including mangrove forests (if weather is bad for diving). Habitat cover will be determined using the 0-6 number or DACFOR scale (Dense; Abundant; Common; Frequent; Occasional; Rare) which can also be converted into a rough percentage cover. Dominant coral genera (see above) will also be recorded in the same format as this will greatly increase the value of the final maps produced. Additionally physical parameters such as depth will also be recorded. We will be mapping the marine reserves, the marine protected area and the un-protected
reefs outside the marine parks.


Each time data is collected it will be placed onto a geo-referenced aerial photograph using Geographical Information System (GIS) software so you can physically see your data being put to use as well as giving you some good experience with GIS.

5.2. Coral Monitoring

This study will also be conducted via SCUBA and/or snorkelling. The study will comprise of a number of pre-positioned 50m transect lines placed by us in pre-determined depth bands along the coral reefs. Divers will be split into groups of 2-3 and will place 1m x 1m quadrats on each side of the transect line recording onto a dive slate any peculiarities/observations within each quadrat, and taking photographs that will be analysed later. We will be doing this at intervals along each transect line. This method is very popular (second only to underwater video transects) as it is less time consuming (beneficial due to time constraints
underwater) and accurate.

Coral Monitoring

The photos will be analysed in the lab where we will be recording percentage cover of dominant coral genera. For the purpose of monitoring, when a transect is completed it will be removed and its position marked with coloured zip ties along conspicuous points every few metres, also visible in the photos. Therefore after a period of time (6 months to 1 year) the transect can be placed back to exactly the same position, sampled again and compared to assess any differences in coral abundances. These can then be linked to anthropogenic pressures such as poor fishing practices or increased sedimentation from oil drilling

Note: If you have your own underwater cameras please do not hesitate to bring them along even though these will be provided.

5.3. Reef Fish and Invertebrate Monitoring

Along the same 50m transect lines as for the corals, other invertebrates such as star fish, sea urchins, and molluscs will be recorded as well as reef fish. Again this will be done in small groups of 2-3. For this the method is slightly different depending on what is to be counted. For small invertebrates such as molluscs etc we will be counting them up to 1m either side of the line swimming at a constant speed. This will be practiced beforehand. For big invertebrates (e.g. Sea Urchins) and small fish (e.g. Clownfish) we increase the distance from the transect line to 2.5m either side and again swim along it and record what is seen. For large fish, such as snappers and groupers, the distance from the line is further increased to 5m either side with the same protocol followed.

Reef Fish Monitoring

The distances from the transect lines will be estimated for the big invertebrates, small fish and large fish categories. For the small invertebrates a transect pole (weighted 2m pole) can be used to swim along with to count individuals that fall within a metre either side of the transect.

5.4. Fish Aggregating Devices (FAD’s)
Fish Aggregating Devices (FAD’s) are man-made objects that are placed in deeper waters (approx. 200m) and are used to attract pelagic fish species. The part that actually attracts the fish will be submerged at 10m (see photo). Currently no research has been conducted on these devices in the Shimoni area. To begin with 3 FAD’s will be placed outside the marine parks in the deeper channels which will be sampled bi-monthly.

Fish Aggregating Devices (FAD’s)

Surveys will be conducted via SCUBA where fish species will be counted along with size estimates (this will be practiced prior). Photographs will also be taken as permanent record. The data will be continuous and will span over 3 years (time taken for FAD to biodegrade) with surveys conducted every 2 weeks.

Comparisons will be drawn between the 3 FAD’s looking at:

Short term:

  • Linking physical factors such as and water temperature and time of year to number and type of fish species along with size estimates
  • Establishing a time frame of fish aggregation per month (max for 3 years until FAD replacement)

Long term:

  • Removing the fishing pressures from around the marine parks and onto FAD sites
  • Monitoring changes in reef fish abundances and FAD catches by local fishermen

Training will be provided on sampling methods, however it is strongly recommended that you familiarise yourself with the coral growth forms, coral genera, and tropical fish species.

Recommended reading

  • Richmond, M.D. A Field Guide to the Seashores of Eastern Africa and the Western Indian Ocean Islands. Sida/WIOMSA. 464pp. ISBN 9987-8977-9-7
  • Bock, K. A Guide to Common Reef Fishes of the Western Indian Ocean & Kenya Coast. 144pp
  • Dytham, C. Choosing & Using Statistics: A Biologists Guide 3rd Edition. Wiley-Blackwell. 320pp (read up on parametric and non-parametric tests, Analysis of Variance, t-tests, and Kruskal-Wallis tests)