Context Some populations of introduced species cause significant undesirable impacts but can also act as reservoirs for genetic diversity. Sambar deer (Cervus unicolor) are ‘Vulnerable’ in their native range and invasive in Australia and New Zealand. Genetic data can be used to determine whether these introduced populations might serve as genetic reservoirs for declining native populations and to identify spatial units for management.

Aim We aimed to identify the provenance of sambar deer in Australia and New Zealand, and to characterise their genetic diversity and population structure.

Methods We used mitochondrial control region sequences and 18 nuclear microsatellite loci of 24 New Zealand and 63 Australian sambar deer collected across continuous habitat in each location. We estimated genetic diversity and population differentiation by using pairwise F_ST, AMOVA, and structure analyses. We compared our data with 27 previously published native and invasive range sequences to identify phylogenetic relationships.

Key results Sambar deer in Australia and New Zealand are genetically more similar to those in the west of the native range (South and Central Highlands of India, and Sri Lanka), than to those in the east (eastern India, and throughout Southeast Asia). Nuclear genetic diversity was lower than in the native range; only one mitochondrial haplotype was found in each introduced population. Australian and New Zealand sambar deer were genetically distinct but there was no population structure within either population.

Conclusions The genetic differences we identified between these two introduced populations at putatively neutral loci indicate that there also may be underlying diversity at functional loci. The lack of population genetic structure that we found within introduced populations suggests that individuals within these populations do not experience barriers to dispersal across the areas sampled.

Implications Although genetic diversity is reduced in the introduced range compared with the native range, sambar deer in Australia and New Zealand harbour unique genetic variants that could be used to strengthen genetic diversity in populations under threat in the native range. The apparent high levels of gene flow across the areas we sampled suggest that localised control is unlikely to be effective in Australia and New Zealand.