Intense herbivory can alter habitat characteristics, and grazing on reproductive structures can reduce plant fitness and long-term population stability. Herbivory on seagrasses is often limited to epiphytes; however, direct grazing has been observed recently in several systems. In San Francisco Bay, California, we documented extensive damage to leaves and especially inflorescences of eelgrass Zostera marina concurrent with blooms of the non-native amphipod Ampithoe valida. Field surveys found peaks of A. valida abundance when eelgrass was flowering, and greater abundance on flowering than vegetative shoots, with particularly high abundances on reproductive structures (spathes) in late developmental stages (with ripe fruits or post seed release). Laboratory experiments showed that A. valida consumed leaf and spathe tissue (as well as whole fruits), but usually preferred spathes to leaves. Spathes are structurally complex and likely provide better habitat, increasing opportunity for consumption. Low field algal abundances do not fully explain eelgrass herbivory, as amphipods grazed eelgrass substantially even when offered algae. When presented with eelgrass from both the amphipod's native (Virginia) and invaded range (California), the latter was consumed at significantly higher rates. Neither nutrient nor phenolic content adequately explain the tissue preference. Greater size of California eelgrass may have promoted incidental feeding on spathes used as habitat, but does not explain a California bias during consumption of structurally simple leaves. Field densities and laboratory consumption rates suggest that this non-native amphipod could remove all seeds in a California eelgrass meadow in 1-3 wk, thus challenging maintenance of genetic diversity and long-term meadow persistence.