Abstract A total of 4845 penaeids belonging to nine species— Metapenaeus anchistus , M. ensis , M. moyebi , M. philippinensis , Penaeus merguiensis , P. monodon , P. semisulcatus , P. latisulcatus and Metapenaeopsis palmensis —were collected by pocket seine monthly over 13 months from mangrove and non-mangrove sites in Guimaras, Philippines. The restricted distribution of the three dominant species— M. ensis and P. merguiensis to the brackish water riverine mangrove, and M. anchistus to the high-salinity island mangrove and tidal flat—is probably related to different salinity and substrate preferences. Abundance and size composition of the major species suggest a strong nursery role for the riverine mangrove (high juvenile densities, relatively small sizes year-round), limited nursery use of the island mangrove (fewer shrimps, larger size ranges, presence of maturing females) and a non-nursery use (e.g. foraging) in the tidal flat. Penaeid recruitment to the river had two peaks in November and May when the average salinity was ∼20 (Practical Salinity Scale) and water temperatures were high (30–31 °C). The spatio-temporal pattern of penaeid species in Guimaras shows partitioning across habitats and seasonal recruitment influenced by physical and biological factors.