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The population genetics of two seagrasses,  Syringodium isoetifolium  and  Thalassia hemprichii  were assessed throughout the Indonesian Archipelago. We genotyped 257 blades of  S .  isoetifolium  at 15 microsatellite loci collected from 14 sampling sites and 406 blades of  T. hemprichii  at 17 microsatellite loci from 16 sampling sites. Once clones were removed, 165 individuals of  S .  isoetifolium  and 389 of  T. hemprichii  were used in downstream analyses. Bayesian clustering methods revealed two genetically distinguishable clusters in each species, although the geographic boundaries of these clusters differed.  Syringodium isoetifolium  has a cluster that is located exclusively on the shallow Sunda Shelf and appears to follow the demarcation defined by Wallace’s line.  Thalassia hemprichii , however, has a genetically distinguishable cluster located within the Banda Sea. The Banda Sea has unique physical oceanographic conditions, which may be driving the observed differentiation in  T. hemprichii . We speculate that historical sea level changes exposing the Sunda Shelf, and the unique oceanographic conditions of the Banda Sea are contributing to the observed population differentiation. The observed genetic differentiation in both species is a possible starting point for speciation.

Population genetic subdivision of seagrasses, Syringodium isoetifolium and Thalassia hemprichii , in the Indonesian Archipelago