This study investigates the diversity and population differentiation of the New Zealand Pot-belly seahorse Hippocampus abdominalis through the utilization of morphological and genetic data. Four microsatellite loci - Habd3, Habd6, Habd7 and Habd9 - and three mitochondrial DNA markers - cytochrome b (814 bp), cytochrome oxidase 1 (624 bp) and control region (404 bp) - in conjunction with quantified morphological features revealed a very high diversity but low population differentiation within New Zealand, suggesting very high levels of gene flow. Some sexual dimorphism was detected, in the terms of shorter snout length and trunk length, and a higher incidence of fronds and spotting in males. A sample size of 166 yielded 31-46 microsatellite alleles and no common multilocus genotypes, and 36-40 new sequences were generated for each mitochondrial DNA marker exposing 14-16 haplotypes, with a maximum of 0.7-2.2% sequence divergence. H. abdominalis were found to be widely dispersed mainly in low density populations. As this species is likely to be facing increased threats from exploitation and habitat degradation in the future it is hoped that this information contributes to the knowledge about H. abdominalis so that future conservation management would be easier to implement.