A total of 256 recent benthic foraminiferal species belonging to 111 genera is identified from 73 carbonate-siliciclastic sediment samples collected along the coast of southern Somalia (Burgao channel) and eastern Kenya (Lamu Archipelago). This represents the first survey of recent foraminifers in this region of East Africa. The sediment samples are representative of different environments (e.g., mangrove flats, tidal channels, restricted shelf, and open shelf), water depths (0–60 m), and salinities (strongly brackish to normal marine conditions). Q-mode Hierarchical Cluster Analysis reveals that nine assemblages can be distinguished; for each assemblage, faunal composition and distribution, diversity indices and dominance are assessed. As predicted by ecological models, there is an overall trend of increasing species diversity from the backwater zone within channels to open marine conditions, and from intertidal to subtidal settings. Salinity, suspended sediment, nutrient levels, and tidal exposure are the most influential factors in determining benthic foraminiferal distribution patterns. An interesting feature is the nearshore contraction of the depth gradient determining the shallower distribution of several larger foraminiferal species, as evidenced by the depth ranges of five species of Amphistegina.