The animal's exquisitely preserved fossils show a creature very similar to modern-day lampreys, having a well-developed sucking oral disk, a branchial basket, at least seven pairs of gill pouches and corresponding gill arches, impressions of gill filaments, and at least 80 myomeres of its musculature.[1] It had the same three phase life cycle found in modern lampreys.[2]
A phylogenetic analysis conducted in 2018 shows that Mesomyzon is the fossil lamprey most closely related to modern taxa, though it is not closely related to any modern group.[3] On the other hand, Brownstein & Near (2022) found it to be a member of the lamprey crown group, most closely related to Petromyzontidae.[4] However, a 2023 study found it again to be a derived stem lamprey, with the earlier Yanliaomyzon from the same region found to be more closely related to modern lampreys. This study also suggested Mesomyzon to be a blood feeder.[2]