These data are from a ChIP-seq experiment using an antibody designed to recognize the centromeric histone CENP-A in the threespine stickleback (Gasterosteus aculeatus) fish. The ChIP-seq was performed on two independent females from the Japan Sea population (also called Gasterosteus nipponicus) and two independent males from the Japan Sea population. The raw Illumina paired-end, 150 bp reads from the chromatin only input (no antibody) and the chromatin immunoprecipitation (IP) using the CENP-A antibody for each individual have been deposited. These data were used to identify the major centromeric repeat sequence in the threespine stickleback.