Abstract Digitaria is a large pantropical genus, which includes a number of economically problematic agricultural weeds. Difficulties in species identification and the circumscription of the genus have previously hindered progress in understanding its evolution and developing a stable classification. We investigate the evolutionary history of Digitaria by combining two approaches: (i) phylogenetic analyses of the currently available Sanger sequence data with previously unpublished sequences mainly from South East Asia, and (ii) newly generated genomic data from low-copy nuclear genes obtained using the Angiosperms353 probe kit, with new data mainly from Madagascar. Both methods gave congruent results. The combination of these results allowed us to confirm a new clade structure within Digitaria lineages, in partial agreement with the previous morphology-based classifications. We confirm that Digitaria as traditionally circumscribed is not monophyletic, comprising Anthephora, Baptorhachis, Chaetopoa, and Chlorocalymma. We present an inference of key character evolution with morphological support for clades with spikelets arranged in binate and ternate groups, with variable trichome morphology, spikelet length, and culm length. Geographical clade structure is also observed. No phylogenetic signal of weedy function was observed.