Abstract
A portion of the cytochrome c oxidase I gene in the caddisfly Orthopsyche fimbriata and in the crayfish Paranephrops planifrons was used to evaluate population genetic differentiation and define conservation units at small spatial scales among neighbouring catchments in the central‐west North Island of New Zealand. Hierarchical analysis of populations from 14 streams found 20 haplotypes in O. fimbriata and 23 haplotypes in P. planifrons . Haplotype diversity was high in most catchments. In O. fimbriata , c. 55% of genetic diversity was distributed among catchments and c. 45% within streams; haplotypes were shared across catchments with only the most northern and southern catchments, separated by c. 100 km, not sharing haplotypes. Paranephrops planifrons had a greater proportion of the total genetic diversity distributed between catchments (c. 72%) and much less within streams (c. 18%); most catchments had unique haplotypes, with only one shared among neighbouring catchments. As a strong disperser, O. fimbriata may have crossed catchments, over evolutionary timescales, but recent deforestation over ecological timescales may prevent ongoing gene flow. In contrast, weak dispersers such as P. planifrons , have no inter‐catchment dispersal, except where there are downstream freshwater connections. Translocation of populations may be necessary to restore areas and should preferably be from within catchments.