Isolated astragali and calcanei of one of the smallest known living or extinct mammals, the geolabidid lipotyphlan Batodonoides powayensis, are identified and described from early and late Uintan (middle Eocene) strata in San Diego County, California. The morphology of the tarsus of Batodonoides appears to be most consistent with arboreal or scansorial locomotion. Prior assessments of geolabidid relationships have allied the group with lipotyphlans, particularly soricids and Solenodon, but the tarsus of Batodonoides shows no particular similarity to any extant lipotyphlan family. Instead, there are unexpected tarsal similarities to the extinct Nyctitheriidae, suggesting that geolabidids may have their origins among Paleocene and Eocene nyctitheres. Results of a phylogenetic analysis are consistent with a relationship either to Solenodon or to Nyctitheriidae. When geolabidids and nyctitheres are allied, the latter group shifts from the euarchontan stem to the lipotyphlan stem, potentially reconciling two divergent views on the relationships of nyctitheres. Batodonoides provides an additional example of the impact of nondental material in challenging established views of the affinities of early Cenozoic ‘insectivores.’