Understanding the genetic diversity of a population is important for understanding population persistence and extinction risk. The long-nosed bandicoot (Perameles nasuta) was once regarded as common throughout its range, but it is unknown whether it is at risk of decline and the genetic diversity in this species has not been assessed. We evaluated the genetic structure and diversity of a P. nasuta population from samples collected during a 6 year demographic study that encompassed a cyclical fluctuation in abundance. Genetic diversity was higher compared to other studies on bandicoot species suggesting the population is not genetically impoverished. We detected significant temporal genetic differentiation suggesting turnover of genotypes. There was no strong evidence for population structuring, indicating a panmictic population. Individual-based spatial autocorrelation analysis generated a similar pattern of relatedness across geographical distances for both sexes suggesting no or limited sex-biased dispersal. This study provides useful baseline genetic data for a large P. nasuta population that is not significantly impacted by introduced predators or habitat destruction.