Ecological variation along the Kenyan coast influences fisheries composition. Kilifi Creek is a unique ecosystem along this coast because it is an open lagoon. A study of the fisheries fauna of Kilifi Creek was conducted between October 2002 and September 2004 at eight sites situated from the mouth to deeper waters within the creek. Monthly sampling for diversity and distribution revealed four crustacean and 63 finfish species. The crustaceans included two prawn species (Penaeus indicus, P. monodon) and two crab species (Portunus pelagicus, Scylla serrata). Crabs were absent from the Konjora site while prawns were absent from the deep sites within the creek. Fish in the order Perciformes dominated the catch at all the sites consisting of 74-95% of the catch. The fishery species landings were higher during the north-east monsoon (October-March) compared to the south-east monsoon (April-September) but Margalef's species richness index (p=0.88), Shannon-Weiner (p=0.6), Pielou's evenness (p=0.05), and Simpson's index (p=0.5) were not significantly different between seasons. Monthly measurements of physico-chemical parameters also revealed that there were significant differences in the phosphate concentration (p=0.0) and temperature (p=0.0) between the north-east and south-east monsoon season but not in other physico-chemical parameters. The finfish composition differed at the different sites and a principal component analysis indicated that water transparency and depth were the main determinants of finfish distribution.