Seagrass are under great stress in the tropical coast of Asia, where Enhalus acoroides is frequently the dominant species with a large food web. Here, we investigate the question of the fine‐scale genetic structure of this ecologically important foundation species, subject to severe anthropogenic disturbance in China. The genetic structure will illuminate potential mechanisms for population dynamics and sustainability, which are critical for preservation of biodiversity and for decision‐making in management and restoration. We evaluated the fine‐scale spatial genetic structure (SGS) and flowering output of E. acoroides, and indirectly estimated the relative importance of sexual versus asexual reproduction for population persistence using spatial autocorrelation analysis. Results reveal high clonal diversity for this species, as predicted from its high sexual reproduction output. The stronger Sp statistic at the ramet‐level compared with genet‐level indicates that clonality increases the SGS pattern for E. acoroides. Significant SGS at the genet‐level may be explained by the aggregated dispersal of seed/pollen cohorts. The estimated gene dispersal variance suggests that dispersal mediated by sexual reproduction is more important than clonal growth in this study area. The ongoing anthropogenic disturbance will negatively affect the mating pattern and the SGS patterns in the future due to massive death of shoots, and less frequency of sexual reproduction.

Symbiotic bacteria associated with benthic invertebrates in seagrass beds play an important role in mediating host adaptability and maintaining ecosystem health; however, the taxonomic composition and functional characteristics of the symbiotic microbiota in these invertebrates remain poorly understood. In this study, the intestinal microbiota of seagrass bed-associated snapping shrimp Alpheus brevicristatus was characterized, and their composition was further compared with that of surrounding seawater and sediment using 16S amplicon sequencing. Our results revealed that the intestinal microbiota were dominated by unclassified Alphaproteobacteria and Vibrio . Compared to that of the environment, the microbiota of shrimp intestines showed lower alpha diversity, yet distinct microbial assemblages. Shrimp intestinal microbiota shared more species with sediment than seawater microbiota, suggesting sediment as a primary microbial source. Beta diversity analysis showed marked differences in microbial structure among habitats. The neutral community model and null model analyses indicated that stochastic processes exerted a significant influence on intestinal microbiome assembly. These findings highlight the complex interplay between host physiology and environmental exposure in shaping intestinal microbiota, providing foundational insights into host-microbe-environment interactions in benthic marine invertebrates.