Sourcing plant species of local provenance (eco-sourcing) has become standard practice in plantcommunity restoration projects. Along with established ecological restoration practices, knowledge of genetic variation in existing and restored forest fragments is important for ensuring the maintenance of natural levels of genetic variation and connectivity (gene flow) among populations. The application of restoration genetics often employs anonymous ‘fingerprinting’ markers in combination with limited sample sizes due to financial constraints. Here, we used two such marker systems, AFLPs (amplified fragment length polymorphism) and ISSRs (inter-simple sequence repeats), to estimate population-level genetic variation of a frequently used species in restoration projects in New Zealand, mahoe (Melicytus ramiflorus, Violaceae). We examined two rural and two urban forest fragments, as potential local source populations, to determine whether the māhoe population at the recently (re)constructed ecosystem at Waiwhakareke Natural Heritage Park, Hamilton, New Zealand, reflects the genetic variation observed in these four potential source populations. Both marker systems produced similar results and indicated that, even with small population sizes, levels of genetic variation at the heritage park were comparable with in situ populations. However, the AFLPs did provide finer resolution of the population genetic structure than ISSRs. ISSRs, which are less expensive and technically less demanding to generate than AFLPs, may be sufficient for restoration projects where only a broad level of genotypic resolution is required. We recommend the use of AFLPs when species with a high conservation status are being used, due to the greater resolution of this technique.