Melaleuca is the second biggest genus (ca. 380 spp.) in the Australian Myrtaceae, after Eucalyptus. Melaleuca species occupy a range of habitats (wetlands to deserts) and are found in all biomes, which make this hyper-diverse genus a good group to carry out evolutionary studies. However, the taxonomy of Melaleuca has been controversial. Melaleuca sensu lato (tribe Melaleuceae) originally included eight other genera. However, with taxonomic changes all of the genera in Melaleuceae were transferred to Melaleuca. To date, the phylogenetic studies based on molecular data have consistently shown that Melaleuca is paraphyletic with respect to the other genera in the tribe. Existing molecular phylogenies of Melaleuca sensu lato have used only a few genetic markers, and the relationships within the genus remain unresolved. With an ultimate aim of estimating a comprehensive phylogeny of Melaleuca using many more loci and more species compared to previous studies, genetic markers for exon capture were developed. Gene trees were assessed to evaluate 196 nuclear and chloroplast markers that were identified. The present study contributes towards more robust estimations of phylogenetic relationships in the genus Melaleuca as well as other genera in Myrtaceae such as Eucalytpus.