A large set of South American fossils belonging to the genus Tapirus has been described on the basis of differences in size and proportions of lower molariform teeth. Nevertheless, the reliability of dental proportions for the diagnosis of fossil tapir species is controversial. In this paper, we describe new fossil material of Tapirus from the Quaternary of Serra da Bodoquena, Southwestern Brazil, comparing it to other fossil and extant specimens of the genus by means of multivariate morphometric analyses of lower molariform teeth linear dimensions. The results of Principal Component Analyses indicate that some of the extant and extinct material attributed to Tapirus fall within the range of variation in size and proportions of lower molariform teeth exhibited by recent species of the genus. Therefore, part of the fossil material attributed to new species or to Tapirus sp. may be referable to the extant species Tapirus terrestris. We conclude that the sole use of lower molariform teeth size and proportions to erect new species of Tapirus may not be reliable, and therefore we advocate caution when describing fossil tapirs exclusively based on these criteria.