The family Malvaceae s. l. is a clade that comprises nine subfamilies. Phylogenetic relationships among them are not completely resolved and are inconsistent among studies, probably due to low phylogenetic informativeness of conventional molecular markers. In the present study, we provide new phylogenetic information for Malvaceae s. l. derived from newly-designed group-specific nuclear markers. By mining transcriptome data from the One Thousand Plants Project (1KP) and publicly available genome information from cotton, cacao, and Arabidopsis, we designed a set of molecular markers of potentially single- or low-copy nuclear genes for Malvaceae s. l. Phylogenetic potential of these new loci was compared to previously applied conventional markers (i.e. plastid trnK-matK region and rbcL gene and the nrDNA ITS region) using the phylogenetic informativeness method. The results show that, when the mined nuclear regions are used in combination, it is possible to resolve relationships at different taxonomic levels within the phylogeny. However, incongruence among nuclear loci is frequent in the group, explaining the prevalence of unresolved phylogenetic relationships.