Olfaction is one of the most commonly used senses for communication among animals and is of particular importance to mother-offspring recognition in mammals. The use of smell in offspring recognition has been well studied, however, we often lack information about the underlying mechanistic basis for olfactory recognition. Using gas chromatography–mass spectrometry (GC–MS), we examine chemical profiles of two different colonies of Australian sea lions (Neophoca cinerea) and assess similarity of chemical fingerprints in mother-pup pairs. This analysis allows us to examine whether a chemical base for phenotype matching exists in this species. Our results showed no GC-detectible mother-offspring similarity in the overall chemical fingerprints, suggesting that direct familiarisation is a more likely mechanism used by Australian sea lion mothers for recognition of their young. Our analysis also demonstrates that colony differences are encoded within chemical fingerprints and appear to be highly influenced by environmental compounds. The study improves our understanding of how Australian sea lion females use odours for selective offspring recognition and the potential importance of environmentally acquired chemical compounds in the overall odour bouquet used in mother-pup interactions.