Many cetacean species are at risk from anthropogenic disturbances including climate change, pollution, and habitat degradation. Identifying cetacean hotspots for conservation management is therefore required. Aotearoa–New Zealand waters are used by 53% of the world’s cetacean species and are a global cetacean diversity hotspot. Using geographic predictions of cetacean taxa, we aimed to identify important areas within New Zealand waters using two methods: estimates of cetacean richness and a spatial prioritization analysis. For both methods, we investigated how varying levels of uncertainty in predictions of the taxa’ occurrence layers would affect our interpretation of cetacean hotspots. Despite some marked spatial differences in distribution of important areas for cetacean diversity, both methods, across all uncertainty scenarios, highlighted six distinct deep offshore regions as important habitat. Generally, inshore areas had lower richness estimates than offshore areas, but these remain important for conservation for species with limited ranges (e.g., the endemic Māui and Hector’s dolphins), and in some places had similar richness values to offshore hotspots. Furthermore, inshore hotspots had lower uncertainty in predicted taxa distribution and richness estimates. The use of two different uncertainty estimates allows the integration of distributional information from differing sources (different modeling methods with varying numbers of cetacean records) to be integrated in a robust and conservative way. Identification of cetacean hotspots with varying levels of uncertainty provides a robust and efficient step toward prioritizing areas for conservation management in a participatory process.