The comparative method in linguistics has enabled to trace phylogenetic relationship among distant languages and reconstruct extinct languages from the past. Nonetheless, it has limitations and shortcomings, which results, in part, from some of its methodological assumptions (particularly, its heavy reliance on the lexicon), but mostly, from the real nature of language change, as languages do not only change by divergence from a common ancestor, but also as a result of contact with non-related languages. At the same time, ongoing research suggests that language change depends not only of the internal dynamics of linguistic systems, but also of factors external to languages, particularly, aspects of human cognition and features of our physical and cultural environments. In this paper, it is argued that the limitations of historical linguistics can be partially alleviated by the consideration of the links between aspects of language structure and aspects of the biological underpinnings of human language, human cognition, and human behaviour. Specifically, it will be claimed that research on human self-domestication (that is, the existence in humans of features of domesticated mammals compared to wild extant primates), which seemingly entailed physical, cognitive, and behavioural changes in our species, can help illuminate facets of the languages spoken in remote Prehistory, the vast time period during which human beings have lived for longer. Overall, we can expect that the languages spoken in that epoch exhibit most of the features of the so-called esoteric languages, which are used by presentday, close-knit, small human communities that share a great amount of knowledge about their environment.