Escherichia coli is commonly used as an indicator of human faecal contamination of ecosytems. There have been limited investigations into the diversity of E. coli communities in wildlife species. The objective of this study was to characterise intra-individual and inter-species phylotype and sub-type diversity in free-ranging pinniped pups, to determine whether a single E. coli colony is representative of overall diversity. Faecal samples (n=213) were collected from Australian fur seal, Australian sea lion and long-nosed fur seal pups between 2018-2021. Faecal swabs from thirty pups (n=10 from each species) were cultured and ten colonies were selected from each culture. We found no significant difference (p>0.05) in either intra-individual or inter-species E. coli phylotype and sub-type diversity. Pup sex was the only host trait found to have a significant effect on phylotype diversity (p=0.0195). The absence of intra-individual and inter-species differences in E. coli diversity at a phylotype level suggests that a single E. coli colony could be used as an indicator of the overall phylotype diversity in these species. These findings can be used to simplify and improve the efficiency of sampling protocols for ongoing monitoring of human-associated phylotypes in free-ranging pinnipeds.