The present study investigated the distribution pattern of six tropical seagrass species on two coral islands in the Spermonde Archipelago, Indonesia. Shoot density, leaf area index, biomass and rhizome length of Halophila ovalis, Halodule uninervis, Syringodium isoetifolium, Cymodocea rotundata, Thalassia hemprichii and Enhalus acoroides were related to water motion and water depth. At research sites with high water motion the seagrass sucession was frequently disrupted by blowouts and moving sandbars, and small seagrass species were dominant. In areas with moderate water motion bare sand patches produced by alpheid shrimp became more prominent, and all six seagrass species were sometimes found forming mixed stands. In sheltered areas mounds and funnels produced by callianassid shrimp were abundant and only the two species T. hemprichii and E. acoroides were present. Assemblages in intertidal areas were dominated by T. hemprichii and C. rotundata. The highest densities of callianassid shrimps were found in deep, sheltered, seagrass-free areas. Shrimp were excluded from experimental plots in one such area and all six seagrass species were transplanted into exclusion, procedural control and zero treatment plots. At the end of a two-year monitoring period, T. hemprichii and S isoetifolium had disappeared from all plots; however C. rotundata, H. uninervis and H. ovalis had successfully established themselves on some of the exclusion plots. There was a marked seasonality, with decreasing water quality during the Northeast monsoon seasons being followed by a decline in shoot numbers inside the plots. Also, seagrass shoots numbers where higher in plots located in shallower water.