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Conserving genetic diversity in wild species is vital for preserving adaptations to local environmental conditions. We conducted a habitat creation project for a flagship European Protected Species of amphibian (northern great crested newt Triturus cristatus) at its north-western range edge in the Scottish Highlands, combining existing knowledge about the species' local habitat requirements and the genetic structure of existing populations. Reconciled by a spatial connectivity model, we determined the best locations for the creation or restoration of 25 ponds to facilitate their natural colonisation, and to reconnect areas with similar genetic makeup whilst preserving differences between populations belonging to separate genetic clusters. A dynamic occupancy model based on data derived from standardised surveys revealed that both detection and occupancy probabilities strongly depended on habitat features known to be locally favourable for T. cristatus. At least 12 of the 25 new ponds were colonised within six years, representing a 26% increase in number of breeding ponds in the region and offsetting a gradual decline in number of pre-existing breeding sites recorded over the last 3 decades. Combining genetic evidence, spatial modelling and historical knowledge with local stakeholder engagement led to a habitat creation and management scheme that has met its immediate and evidence-based conservation goals in a way which is transferable to a range of different systems. [ABSTRACT FROM AUTHOR]