Ligia are a globally distributed genus of isopods mostly found in the intertidal region of rocky coastlines. Due to their poor dispersal capabilities, Ligia in isolated locations often harbor highly unique genetic lineages. In some instances, these lineages have been shown to represent cryptic species (i.e., two or more morphologically similar species recognized as a single species). High levels of cryptic diversity within Ligia have been reported from the Hawaiian Islands, the Caribbean region, Southern Africa, the Seychelles, amongst others. We used molecular methods to characterize populations of Ligia novizealandiae from Aotearoa New Zealand and thus determine if cryptic diversity is found within this remote region of the Southwest Pacific. We extracted DNA from individuals collected in six localities from Te Ika-a-Māui / North Island of Aotearoa New Zealand. Three mitochondrial genes (CO1, 16S rDNA, 12S rDNA) and two nuclear genes (NaK, 28S rDNA) were sequenced from each individual. Phylogenetic reconstructions indicate the presence of three distinct and well-supported L. novizealandiae lineages: (a) one found in four localities on the western coastline, (b) another found at Moa Point at the southern end of the island, and (c) a lineage found at Waiwera Beach in the northeast. These lineages are highly divergent, as estimates of evolutionary divergence between 16S rDNA sequences using the Kimura 2-parameter amongst genetic range from 13.5% to 29.7% and exceed those reported for comparisons between Ligia species. To further our understanding of cryptic diversity within Aotearoa New Zealand, additional sampling will need to be conducted on the east coast of Te Ika-a-Māui / North Island and on Te Waipounamu / South Island. Further analysis will need to be completed to identify any additional lineages and determine whether these lineages represent new species.