Understanding how genetic variation within a particular species is spatially structured is important for knowing how populations are connected and how landscape configuration affects population connectivity. Landscape genetics provides an ideal toolbox to determine patterns and processes structuring populations. These techniques were applied to two species of New Zealand skink, the common skink Oligosame nigraplantare polychorma and McCann’s skink Oligosoma maccanni, to investigate how these populations are structured in Canterbury and Otago, New Zealand. Specific objectives for this study were (1) to determine the genetic structure of both species, (2) to determine the influence of landscape features on genetic structure, (3) to determine how geography and genetic structure influence patterns of morphological variation and (4) to use this information to recommend conservation management plans for these species. Microsatellite genotyping was used to determine genetic structuring for both species. Distance matrices were created for genetics, land use, Euclidean distance and morphology. Population genetic structure was calculated using GenAlEx. All realtionships between distance matrices were analysed using Mantel and partial Mantel tests. The results showed signicant genetic structure in both species. Landscape and geographic distances had a significant relationship with genetic distance for the common skink, but not for McCann’s skink. Morphology was not correlated with genetic distance in either species, but there was some correlation between geography and morphology. Based on this, the study has highlighted that populations of congeneric species, that are sympatric and ecologically similar, are not necessarily influenced by the same landscape features. This has implications for conservation, indicating that species-specific conservavtion strategies should be applied.