We assessed differences in the otolith microchemistry of koi carp, a colour variant of the invasive common carp Cyprinus carpio, at various locations in the Waikato region of New Zealand. Although koi carp are abundant here, little is known about where and in what habitats they breed. We investigated the feasibility of determining the natal habitats of adult koi carp (in the Waikato River, selected tributaries, and riverine lakes in the catchment) using otolith elemental signatures and employing laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS). Differences in elemental concentrations in water among the sites indicated that variation in otolith microchemistry was likely. Ratios of manganese (Mn), rubidium (Rb), strontium (Sr), and barium (Ba) to calcium (Ca) in otolith edges differed significantly among the sites, and Sr:Ca in the water and otoliths was positively correlated. A discriminant function analysis using Rb, Sr, and Ba accurately classified the otolith edge signatures of koi carp from some locations, but the otolith signatures of koi carp caught from adjacent locations were often indistinguishable. This suggests that our results could have been confounded by either (1) recent movement of koi carp or (2) a lack of differences in water chemistry among sites. Taken together, these results demonstrate that otolith microchemistry can be used to test retrospectively for koi carp migration between sites on a broad scale in the Waikato region, but fine-scale movements may not be detectable.