The tiny dragonfly, Nannophya pygmaea (Odonata: Libellulidae) is one the smallest dragonflies in the world and listed as a second-degree endangered wild animal in Korea. We developed microsatellite markers and applied selected markers to South Korean populations to understand population genetic characteristics, along with two mitochondrial DNA (mtDNA) gene sequences (COI and ND5). Two mtDNA-based population genetic analysis indicates substantially reduced genetic diversity in an island population (Muuido) compared to others. On the other hand, population-based FST and RST consistently support that N. pygmaea populations are overall well interconnected with a relatively high gene flow. These results may collectively indicate that N. pygmaea populations in South Korea may have rather larger population size than we previously acknowledged based on a single-locus mtDNA sequence and field observation.