To determine the evolutionary history, relationships and distinctiveness of allopatric populations of Hispaniolan solenodon (Solenodon paradoxus), a highly threatened Caribbean ‘relict’ mammal, to understand spatio-temporal patterns of gene flow and the distribution of diversity across complex large island landscapes and inform spatial conservation prioritization. Historical and modern-day solenodon specimens were analysed from sampling localities across Hispaniola, representing this geotectonically complex island's distinct northern, south-eastern and south-western biogeographic provinces. We successfully amplified mitochondrial cytochrome b and control region sequences from 34 solenodon samples. Bayesian phylogenetic analyses were applied to assess the relationship between these sequence data, and coalescent simulation and approximate Bayesian computation were used to identify which model of solenodon intra-island demographic history best explains the observed patterns of variation. We also conducted morphometric analysis of 110 solenodon specimens to investigate whether allopatric Hispaniolan populations can be differentiated using craniodental characteristics. Unique haplotypes were identified in solenodon samples from each biogeographic region, with no haplotype sharing between regions. Higher marginal posterior probability values were found for a three-population model comprising allopatric northern, south-eastern and south-western Hispaniolan populations, with exceptionally low migration rates inferred between all populations, indicating that they are genetically isolated. Modal estimates of long-term effective female population size are extremely low for south-western and south-eastern populations. Morphometric differentiation is observed between all three populations. Evolutionary differentiation of Hispaniolan solenodons into three distinct populations is congruent with phylogenetic patterns observed in several other Hispaniolan species, with population isolation possibly associated with past marine transgression. We interpret these populations as distinct subspecies, with the two genetically impoverished southern subspecies particularly vulnerable to environmental change. Our improved understanding of Hispaniolan solenodon evolutionary history provides an important baseline for identifying wider patterns of intra-island diversification and prioritizing conservation attention for evolutionarily significant populations.