Archaeologists working in the tropical Pacific have demonstrated the feasibility and value of including fish vertebrae in midden analyses, and recent New Zealand studies draw similar conclusions. This work provides an illustrated guide to the identification of vertebrae from key New Zealand fish taxa and shows the effects of including vertebrae on a large fishbone assemblage from southern New Zealand. We note major differences between New Zealand and tropical Pacific assemblages resulting from the inclusion of vertebrae. Unlike the Indo‐Pacific taxa of the tropical Pacific, no New Zealand species have been shown to be sensitive to the inclusion of vertebrae. In both places including vertebrae results in changes in relative abundance and rank order but in New Zealand this is a function of processing practices, not fishing behaviours. This work serves to highlight changes in the Polynesian fishing adaption following the colonisation of New Zealand.