Gerromorpha Popov, 1971 is a fascinating and diverse insect lineage that evolved about 200 Mya ago to live their entire life cycle on the air-water interface, and have since colonised all types of aquatic habitats. In this infraorder, the subfamily Halobatinae Bianchi, 1896 is particularly interesting because some species have evolved and adapted to live out in the open ocean. Attempts have been made to reconstruct the evolutionary phylogeny of this subfamily, but the use of few partial gene sequences recovered only a handful of well-supported relationships within the subfamily, thus limiting evolutionary inferences. Fortunately, the emergence of high-throughput sequencing technologies has enabled recovery of more genetic markers for phylogenetic analyses. In this study, we applied genome skimming to obtain mitochondrial and nuclear genes from low-coverage whole-genome sequencing of 85 specimens for reconstructing a well-supported phylogeny, with particular emphasis on Halobatinae. We confirmed that Metrocorini Matsuda, 1960 is paraphyletic, where Esakia Lundblad, 1933 and Ventidius Distant, 1910 are more closely-related to Halobatini Bianchi 1896, than Metrocoris Mayr, 1865 and Eurymetra Esaki, 1926. We also found that the Ventidius is paraphyletic and is in need of taxonomic revision. Ancestral state reconstruction also suggested that the Halobatinae evolved progressively from limnic to coastal habitats, eventually attaining a marine lifestyle in three distinct lineages, especially in the genus Halobates Eschscholtz, 1822, and that the oceanic lifestyle in Halobates evolved thrice. Our results show that genome skimming is a powerful and straightforward approach to recover genetic loci for robust phylogenetic analysis in non-model insects.