The range of the tammar wallaby (Macropus eugenii) has decreased substantially in Australia in recent times. Because two introduced populations in New Zealand may have descended from a now-extinct Australian population(s), we investigated their origins using a novel approach. We combined data from seven highly polymorphic microsatellite markers with simulation modelling to infer the history and conservation value of the New Zealand populations. The microsatellite alleles in one New Zealand population (Rotorua) are merely a subset of those in the other (Kawau Is.), suggesting Rotorua had no immigrants from an independent source. However, in the Kawau Is. population (sample size 33–37), 37 alleles were absent that were present in the Kangaroo Is. (South Australia) population at frequencies ranging from 1–40%. The probability of those alleles being lost during a founding event from Kangaroo Is. was investigated using a program that simulates the genetic consequences of population size bottlenecks. Use of realistic bottleneck parameters resulted in probabilities approaching zero that the observed allele deficiencies in the Kawau population could have occurred randomly, identifying the New Zealand tammar wallabies as descendants of a distinct taxon that is no longer extant in Australia.