Seagrasses provide a variety of ecosystem goods and services, but they are subjected to frequently anthropogenic disturbances. In this study, we genotyped samples collected from Zostera japonica meadows with dramatic fluctuations in the area in order to understand the distribution of genetic variation within and among populations.

We collected samples from eight extant populations along coastal areas of southern China. Ten polymorphic microsatellites were adopted to genotype the samples. Parameters of genetic diversity and differentiation were calculated with general software.

High levels of genetic diversity were found in the studied populations, suggesting that the effective population size has not decreased significantly, which was supported by no signs of recent bottlenecks. High genetic diversity reflects an important role of sexual seedling recruitment in Z. japonica populations. We found a significant relationship between genetic differentiation and the shortest sea surface distance of populations, suggesting that ocean currents play a critical role in shaping the genetic structure of Z. japonica populations. STRUCTURE software analysis clustered the eight populations into two groups: western and eastern populations separated by the Qiongzhou Strait/Leizhou Peninsula, hinting that there was very limited gene flow through the narrow strait in this marine plant. Four populations had high contribution diversity and, thus, high priority for in situ conservation.