Pholcid spiders have long been classified into five subfamilies, and this framework ultimately dates back to Eugène Simon’s non-phylogenetic system of 1893. While subfamily relationships and compositions have been updated extensively over the last decades, no new subfamily had to be erected for any of the hundreds of new species newly described since Simon. Here we report two new species from semi-arid Brazilian Caatinga: Caipira mineira Huber sp. nov., and Caipira baiana Huber sp. nov. Genomic data strongly support their sister-group relationship; we thus join them conservatively in a single genus, Caipira Huber gen. nov., even though they show some remarkable morphological differences. This genus is sister to a large clade including all pholcid subfamilies except Pholcinae and Smeringopinae, which necessitates the erection of a new subfamily: Caipirinae subfam. nov. In addition, we formalize the separation of the genus Artema from ‘other Arteminae’. This had previously been suggested by multi-locus genetic data, and is strongly supported by new genomic data. Arteminae is newly circumscribed to include only Artema and Priscula, and the name Physocyclinae subfam. nov. is proposed for ‘other Arteminae’. Pholcidae is thus divided into seven subfamilies, with the following relationships suggested by genomic data: (Pholcinae, Smeringopinae), (Caipirinae, ((Arteminae, Ninetinae), (Physocyclinae, Modisiminae))). Finally, we tested the hypothesis that the Chilean genus Aucana is the closest relative of the new Brazilian species. This is strongly rejected; Aucana is resolved as the only known South American representative of Physocyclinae.