Understanding diversity has been a pursuit in evolutionary biology since its inception. A challenge arises when sexual selection has played a role in diversification. Questions of what constitutes a “species”, homoplasy versus synapomorphy, and whether sexually-selected traits show phylogenetic signal have hampered work on many systems. Peacock spiders are famous for sexually selected male courtship dances and peacock-like abdominal ornamentation. This lineage of jumping spiders currently includes over 90 species classified into two genera, Maratus and Saratus. Most Maratus species have been placed into groups based on secondary sexual characters, but evolutionary relationships remain unresolved. Here we assess relationships in peacock spiders using phylogenomic data (UCEs and RAD-seq). Analyses reveal that Maratus and the related genus Saitis, are paraphyletic. Many, but not all, groups within a “core Maratus” clade are recovered as genetic clades but we find evidence for undocumented speciation. Based on original observations of male courtship, our comparative analyses suggest that courtship behavior and peacock-like abdominal ornamentation has evolved sequentially with some traits inherited from ancestors with others evolving repeatedly and independently from “simple” forms. Our results have important implications for the taxonomy of these spiders, and provide a much-needed evolutionary framework for comparative studies of sexual signal character evolution.