The ant genus Myrmelachista (Hymenoptera: Formicidae: Formicinae) has a Neotropical distribution and includes 69 described species and subspecies, with many more undescribed. Within the genus, species can be broadly divided into two mains ecological groups: 1) opportunistic inhabitants of dead and live stems, and 2) specialist symbionts engaged in mutualistic associations with a set of plant species. For the latter, species were previously thought to form a clade within the genus. However, our phylogenomic analyses have revealed several instances of independent evolution of mutualistic assemblages, emphasizing the difficulty of distinguishing species from each other based solely on morphology. Additionally, when we investigated the divergence times for the group, our analyses estimating that most mutualistic species arose relatively recently (late Pliocene-early Pleistocene), suggesting a rapid diversification of those taxa. To shed light on species boundaries, we applied an integrative approach to delimit Myrmelachista species based on target enrichment of ultraconserved elements (UCEs), mitochondrial COI (cytochrome C oxidase I) barcodes, queen and worker morphometrics, and natural history data. We assess concordance among principal component analysis (PCA) clustering of morphometric data, gene-tree and SNP-based species tree inference, molecular methods of species delimitation (STACEY and BPP), and fieldwork information. Our results highlight the utility of UCEs as markers for resolving shallow-scale evolutionary relationships. We also observed that we could morphologically diagnose otherwise difficult species by integrating well-curated natural history data with different analytical approaches.