Otter populations declined drastically across many areas of England and Wales during the 1960s to 1980s. The main cause of this decline is thought to have been high concentrations of organic pollutants, in particular PCBs and dieldrin. Here we look at the health of the present day otter population, focussing on the numbers of otters, the genetic diversity of populations and investigating a possible new organic pollutant threat, polybrominated diphenyl ethers (PBDEs). A non-invasive spraint genotyping study of the otter population inhabiting the River Camel in Cornwall not only revealed that the river was capable of supporting a minimum number of 12 otters over a 9 month period, but gave insight into the ranges and genetic relationships of the individuals using the river system. A further population genetic study was carried out focussing on the River Itchen in Hampshire, a population which declined drastically to just a few isolated individuals before receiving otters through a captive breeding programme. Microsatellite genotyping of tissue samples showed the River Itchen population to be relatively diverse, indicating a successful population recovery, and haplotype analysis reveals that captive bred otters have successfully bred within the River Itchen population. However, haplotype analysis also indicates that the otters used to found the captive breeding programme were unlikely to have originated from a native British population. Concentrations of PBDEs in otters rival the high concentrations observed in many marine mammal species and are approaching the concentrations of PCBs and DDTs already observed in otters. The profile of the PBDE congeners found shows that lower congeners show relative concentrations similar to those observed in many other species of biota, with high BDE-47 dominating the profile and BDE-99 and -100 also found at significant concentrations. Otters also contain relatively high concentrations of the congeners BDE-153 and BDE-209, a trend generally typical of terrestrial top predators. In summary, the otter populations studied appear to be recovering well. However, increasing concentrations of PBDEs may cause problems for otter populations in the future.