Flower and fruit production of the abundant, tall, long-lived, dioecious, surface-pollinating seagrass species Enhalus acomides (L.) Royle were estimated at seven sites in the reef flats off Bolinao (NW Luzon, The Philippines) featuring different fragmentation of the seagrass meadows. Fragmentation of the seagrass meadow was quantified as cover of E. acoroides and all seagrass species present in 20 x 20 m plots. E. acoroides and overall seagrass cover were correlated positively. The proportion of female flowers of E. acoroides that developed a fruit increased sharply as overall seagrass cover was around 50%. Apparent sex ratio bore no relationship with overall seagrass cover. This threshold-type of relationship suggests that fragmentation of seagrass meadows can have a major effect on the reproductive output of this species. A possible mechanism underlying these results would be a non-linear increase of the efficiency of trapping the surface-dispersed pollen with increasing seagrass canopy density. This provides the first evidence based on real data that fragmentation can affect the population dynamics of seagrass species.