Caridean shrimp were used as a model group to investigate the effects of seagrass floral habitat complexity on Indo-Pacific fauna. Relationships between shrimp and seagrass habitat characteristics were explored using both multivariate and multiple linear regression modelling approaches. Epifaunal shrimp assemblages were sampled in the Wakatobi Marine National Park, Indonesia. Seagrass habitat complexity had a significant positive impact on shrimp abundance (F_3,59 = 17.51, P < 0.001) and species richness (F_3,59 = 10.88, P < 0.001), while significantly altering shrimp assemblage structure (ANOSIM global R = 0.397, P < 0.001). In contrast to studies from other bioregions and faunal groups, species diversity and evenness were inversely related to habitat complexity. Changes in shrimp abundance, diversity and assemblage structure with habitat complexity are considered to reflect changes in individual species habitat specialisation. High complexity habitats were dominated by habitat specialists, whereas low complexity seagrass had higher numbers of habitat generalists. Generalist species may be more adapted to the reduced food availability and increased predatory pressures associated with reduced habitat complexity. Although similar patterns were observed at all sites, inter-site differences in shrimp abundance were observed. This indicates that although the present study demonstrates the importance of small-scale changes in seagrass habitat complexity to faunal assemblages, other factors related to larger spatial-scales are also important.