*2.2. Monitoring of Coral Reef Fishes and Corals*

Corals and fishes were surveyed at ten different reef sites on Chale Reef, with some transects on the seaward side of the reef and some on the landward side to provide a range of different reef conditions. Within each site, three belt transects of 5 × 50 m were placed haphazardly, but mostly parallel to the shore. Transects were located at least 150 m apart so as to achieve reasonable independence of the samples. Sampling was conducted around low tide (<70 cm) to provide standardized assessment conditions, while time of day and weather conditions varied through the study. During each survey, one person snorkeled in front, counting fishes using established underwater visual survey methodology [46], while a second person swimming behind laid out a 50 m tape along a track following the first snorkeler (this sequence was followed to avoid the fish being disturbed before they could be counted). For this study, eight fish families, which are known indicators of coral reef biodiversity, were preselected for the census: *Scaridae*, *Acanthuridae*, *Siganidae*, *Ephippidae*, *Pomacanthidae*, *Chaetodontidae, Lutjanidae*, and *Serranidae*, all of which are moderately speciose on Kenya's southern coast [47]. Additionally, on the first half of the transect (25-m length) the hard corals were identified to genus level and the colonies counted.
