Podarcis lilfordi is an endemic lizard found on islands and islets off the coast of Mallorca and Menorca (including the Cabrera archipelago) in the Balearic Islands, which is extinct on the two main islands themselves. Analyses of mtDNA revealed four unconnected parsimony networks. These represented (I) all Menorcan populations, (II) Dragonera, Malgrats and Toro islands (Western Mallorca), (III and IV) the remaining populations from Cabrera and Mallorca. We applied NCPA to evaluate its utility in understanding the genetic sub-structure. Within network I, contiguous range expansion was inferred for both main clades. Populations from western Mallorca (II) have undergone historical allopatric fragmentation events following isolation around the start of the Pleistocene. Clades within networks III and IV showed some allopatric fragmentation and restricted gene flow (isolation by distance) among islands from Cabrera, as well as long distance dispersal between the Cabrera archipelago and southern Mallorca. The NCPA strongly supports the importance of allopatric fragmentation, with some additional support for range expansion. The primary advantage of the NCPA approach was to provide statistical support for these inferences.