Genetic diversity and population structure of New Zealand populations of the pot-belly seahorse Hippocampus abdominalis were explored via three mitochondrial DNA markers (814 bp of cytochrome b, 624 bp of cytochrome oxidase 1 and 404 bp of the control region) and four microsatellite loci (Habd3, Habd6, Habd7 and Habd9). These markers revealed between 0.7Á2.2% sequence divergence and 32Á46 alleles with low differentiation among populations around the coastline. In total, 169 seahorses (79 females and 90 males) were sampled with 36 sequences generated for each marker and 166 genotypes attained. It is hoped that this new knowledge will aid in the development of future conservation management.