Most scleractinian coral species are widely distributed across the tropical and subtropical Indo-Pacific. However, the genetic connectivity between populations of corals separated by large distances (thousands of kilometers) is not well known. We analyzed variability in the nucleotide sequence of the internal transcribed spacer-1 (ITS-1) of the nuclear ribosomal gene unit in the ubiquitous coral Stylophora pistillata, across the western Pacific Ocean. Eight populations from Japan, Malaysia, and the northern and southern Great Barrier Reef (GBR) were studied. Phylogenetic analyses and analysis of molecular variance (AMOVA) clearly revealed that there is panmixia among these coral populations. AMOVA showed that ITS-1 sequence variability was greater within populations (78.37%) than among populations (12.06%). These patterns strongly suggest high levels of connectivity across the species' latitudinal distribution range in the western Pacific, as is seen in many marine invertebrates.