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We have shown that anomalous forms of highly conserved protein families are found within a derived subset of genomes, in this case, seryl- and threonyl- amionacyl-tRNA synthetases, have a phylogenetic history consistent with these genes being horizontally transferred from very ancient lineages that diverged earlier than the ancestor of the 3 known Domains of life. Observing these kinds of ancient “hypnolog” genes is predicted by coalescent theory, and supports models that the earliest cellular life had a diversity rooted deeper than the Last Universal Common Ancestor (LUCA). This result also implies that these other deep lineages survived for some time alongside the extant Domains, likely at least into the Archean, so that genes could continue to be transferred to more derived lineages within Archaea and Bacteria. Furthermore, this work illustrates that LUCA is not necessarily the singular ancestral source of all ancient gene families.