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This study examined the variation of macrofaunal communities in sea grass beds along a pollution gradient in Bolinao, northwestern Philippines. We established four stations and compared the diversity and abundance of macrofauna between them. The Shannon diversity index in the least polluted station was more than twice higher than that in the most polluted one. Abundance was more than thrice higher in the most polluted station. The species composition generally varied, with community difference explained largely by the predominance of the filter-feeding bivalve Gafrarium pectinatum and polychaete Capitella capitata. Species heterogeneity was reduced along the pollution gradient by approximately 19% from the least polluted to the most polluted station. This reduction indicates biodiversity alteration, which has a significant impact on ecosystem functioning. Aspects of species heterogeneity should be considered in environmental impact assessments and the management of coastal areas encountered with anthropogenic disturbances.

Many marine species have a pelagic larval phase that undergo dispersal among habitats. Studies on marine larval dispersal have revealed a large variation in the spatial scale of dispersal and self‐recruitment. However, few studies have investigated the influence of types of coastline (e.g., bay vs. open coast) on marine larval dispersal. Bays or lagoons generally enhance the retention of larvae, while larvae are more likely to be flushed by strong currents in open coasts. To examine associations between larval dispersal, coastline type, and hydrodynamics, we compared fin‐scale dispersal patterns, self‐recruitment, and local retention (LR) of two anemonefishes (Amphiprion frenatus and Amphiprion perideraion) between a semi‐enclosed bay and an open coast in the Philippines combining genetic parentage analysis and biophysical dispersal modeling. Contrary to our expectations, parentage analysis revealed lower estimates of self‐recruitment in the semi‐closed bay (0%) than in the open coast (14–15%). The result was consistent with dispersal simulations predicting lower LR and self‐recruitment in the semi‐closed bay (0.4% and 19%) compared to the open coast (2.9% and 38%). Dispersal modeling also showed that cross‐shore currents toward offshore were much stronger around the semi‐closed bay and were negatively correlated with LR and self‐recruitment. These results suggest that stronger cross‐shore currents around the semi‐closed bay transport anemonefish larvae to the offshore and mainly contributed to the lower self‐recruitment. Our results highlight importance of hydrodynamics on larval dispersal and difficulty in predicting self‐recruitment from coastline type alone.