In recent times, the apparent population decline of the southern bent-wing bat (Miniopterus schreibersii bassanii) at Bat Cave, Naracoorte has been ascribed to pesticide use in the region, following the finding of organochlorine and orgaonophosphate insecticide residues in bat guano. Adult southern bent-wing bats were collected from Bat Cave and Starlight Cave in 2003. Organochlorine contaminants were detected in all carcass samples: p,p′-DDE was by far the most dominant contaminant with concentrations ranging from 11 000 to 59 000 ng g−1, followed by p,p′-DDT (110–1600 ng g−1), p,p′-DDD (35–620 ng g−1), ∑PCBs (33–490 ng g−1), ∑chlordane and related compounds (7.9–270 ng g−1), HCB (1.6–120 ng g−1), HP epox. (3.1–230 ng g−1), TCPMOH (3.8–38 ng g−1), ∑HCHs (1.4–9.6 ng g−1), and TCPMe (0.1–4.2 ng g−1) (all values on lipid-weight basis). No significant difference in DDE, DDD, DDT, ∑DDT, ∑PCB, trans-chlordane, heptachlor epoxide, trans-nonachlor, α-HCH, β-HCH, γ-HCH, TCPMOH or TCPMe concentrations were observed either between sexes within sites, or between sites (p > 0.05). However, there were significant differences in HCB and oxychlordane concentrations between sexes and between sites (p < 0.05), between site differences in cis-nonachlor concentrations in male bats (p < 0.05), and cis-chlordane concentrations between sexes at Starlight Cave, and between males of each site (p < 0.05). There were also significant differences in the liver concentrations of some metals between sexes within sites (Ag, Cd, Co, Cu, Pb, Se, Zn), and between sites (Ag, Cd, Co, Cu, Hg, Pb, Se, V, Zn). Clustering or grouping of sites was observed when the OC data was expressed on a lipid-weight basis. These inter-site differences in OC concentrations reflect local exposure over a period of time, and do not unambiguously support any suggestion that we are witnessing incipient speciation. However, for conservation purposes, it may be prudent to assume that there are two sub-populations of M. s. bassani feeding in different locations in this region of southern Australia, rather than the single homogeneous population suggested by genetic studies.