Seagrasses are recognized for their fundamental and ecological functions in coastal environments. Movement ecology and dispersal mechanism of organisms are hypothesized to have a profound significance for the dynamics and resilience of populations and ecosystems. We tested this hypothesis by comparing the genetic diversity and fine-scaled structure of co-occurring seagrass populations of Thalassia hemprichii and Cymodocea serrulata, which differ in their survival strategy and movement ecology. Two hundred eighty-four and two hundred sixty-three individuals of T. hemprichii and C. serrulata from 6 seagrass meadows along Leyte, Philippines were genotyped using 15 and 9 microsatellite markers, respectively. Thalassia hemprichii was observed to have higher genotypic diversity, while clonal elongation was more pronounced for C. serrulata. Repeated seedling recruitment followed by rhizome elongation was observed as an important strategy of resilience and indicated the complementary importance of both sexual and asexual reproduction of these species. Moreover, fine-scale spatial structure analysis revealed that repeated seed recruitment and pollen flow occurred locally, yielding higher kinship values at very close distances of < 5 m, indicating its importance for the maintenance of genetic diversity. An individual based STRUCTURE analysis showed three putative gene pools for both species. Overall, our findings have important implications for understanding the processes and dynamics of populations before conservation efforts. Depending on the strategy of the species, efforts should focus on preserving natural expansion of existing beds and enabling local seed recruitment for successful conservation.