||I employed multi-gene phylogenetic analyses using nuclear (RAG-1, PDC) and mitochondrial (ND2, 16S) genes to determine relationships among 180+ specimens representing all recognized species, and all but two putatively new species detected by allozyme data. Three analytical methods (Maximum Parsimony, Maximum Likelihood and Bayesian Inference) were employed and they retrieved a monophyletic New Zealand clade, most closely related to the Australian Diplodactylidae. Hoplodactylus is paraphyletic and composed of two morphological groups: a broad-toed clade, consisting of the speciose, wide-ranging H. maculatus clade; and a narrow-toed clade, composed of five monophyletic groups: Naultinus , the H. pacificus and H. granulatus clades, and the distinctive species, H. rakiurae and H. stephensi . My data support recognition of 17 new species (35 total). Biogeographic patterns suggest that earth history events influenced cladogenesis and distribution patterns of New Zealand geckos. This study delimits operational taxonomic units upon which informed conservation priorities can be based.