Phylogenetic reconstructions can be difficult in recently diverged lineages, such as those found in the family Cactaceae, due to a lack of phylogenetic signal and an excess of incomplete lineage sorting in genetic data.  Large polytomies may result from the absence of phylogenetic signal, while incomplete lineage sorting can produce incongruent phylogenetic relationships with with morphology and the group's evolutionary history. To overcome these obstacles, multiple independent loci from different genomes should be combined with phylogenetic approaches that consider the heterogeneity of gene trees. Melocactus Link & Otto (Cactaceae), a widely distributed genus in South America and Caribbean, has not been comprehensively studied using genetic data. We have generated a multi-locus dataset using high-throughput sequencing of target nuclear loci, which allowed a robust phylogenetic inference. Our results partially support the taxonomic groups proposed for Brazilian species based on morphological variation and ecological characteristics, with a divergence time estimated in the Pliocene. These findings provide insight into the evolutionary history of this genus and will be useful in future studies, such as biogeographical and comparative phylogenetic approaches.