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. ensisandP. merguiensisto the brackish water riverine mangrove, andM. anchistusto 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.