Intraspecific genetic differentiation reflects processes that underpin biodiversity in deep-sea habitats. We examined the spatial genetic structure of epibenthic amphipod taxa from upper bathyal depths (200–1200 m) along New Zealand's continental margins. Genetic variability in amphipods was assessed using cytochrome c oxidase I (COI) to characterise inter-regional diversity and phylogeographic patterns in the Chatham Rise and Challenger Plateau to the east and west of New Zealand, respectively. Automatic barcode gap discovery methods identified 263 MOTUs, of which 14 were detected in both regions. Population genetic analyses found contrasting patterns of diversity among different MOTUs within and between regions. Overall, a pattern of increasing genetic differentiation (K2P distances) with decreasing depth was observed between regions. Genetic differentiation was highest among MOTUs found at shallow depths, while taxa from deeper waters showed little evidence of divergence. Our results suggest that intraspecific genetic diversity is correlated with amphipod family traits, particularly dispersal abilities inferred from habitat preferences (infaunal, epibenthic or pelagic) and may also be linked to regional geological history. Such insights have important implications for regional-scale patterns of diversity associated with local processes in promoting differentiation among populations of bathyal amphipods on New Zealand's continental margins.

种内遗传分化反映了深海栖息地生物多样性的基础过程。我们研究了沿新西兰大陆边缘上层深海（200-1200 m）的表皮两栖动物类群的空间遗传结构。使用细胞色素c评估两栖动物的遗传变异性氧化酶I（COI）分别表征了新西兰东部和西部的查塔姆高原和挑战者高原的区域间多样性和植物地理特征。自动条形码间隙发现方法可识别263个MOTU，其中两个区域均检测到14个。人口遗传分析发现，区域内和区域之间不同MOTU之间的多样性形成了鲜明对比。总体而言，观察到区域之间的遗传分化（K2P距离）随着深度减小而增加的模式。在浅层发现的MOTU中，遗传分化最高，而来自较深水域的分类单元几乎没有发散的迹象。我们的结果表明，种内遗传多样性与两栖动物的家庭特征有关，特别是从栖息地偏好中推断出的传播能力（不育，表皮的或上层的），也可能与区域地质史有关。这些见解对于与本地过程相关的区域尺度多样性模式具有重要意义，可促进新西兰大陆边缘的深水两栖动物种群之间的分化。