Coral reef associated marine invertebrates, such as the blue sea star Linckia laevigata, have a life history with two phases: sedentary adults and planktonic larvae. On the one hand it is hypothesised that the long pelagic larval duration facilitates large distance dispersal. On the other hand, complex oceanographic and geographic characteristics of the Visayan seascape could cause isolation of populations. The study aims to investigate the genetic diversity, genetic population structure and gene flow in L. laevigata to reveal connectivity among populations in the Visayas. The analysis is based on partial sequences (626 bp in length) of the mitochondrial cytochrome oxidase I gene (COI) from 124 individuals collected from five localities in the Visayas. A comparative analysis of these populations with populations from the Indo-Malay Archipelago (IMA) published previously is also presented. Genetic diversity was high (h = 0.98, p = 1.6%) and comparable with preceding studies. Analyses of molecular variance (AMOVA) revealed a lack of spatial population differentiation among sample sites in the Visayas (FST-value = 0.009; P > 0.05). The lack of genetic population structure indicates high gene flow among populations of L. laevigata in the Visayas. Comparative analysis with data from the previous study indicates high connectivity of the Visayas with the central part of the IMA.