Recent years have seen an increase in the number of studies that use DNA sequence information in addition to morphological methods, as the latter alone can be inadequate for morphologically similar, cryptic species. Marine onchidiid slugs (Mollusca: Gastropoda: Onchidiidae), which commonly inhabit intertidal environments and have a near-global distribution, comprise 11 genera and 86 described species. Singapore has 19 recorded species of onchidiids with Peronia verruculata (Cuvier, 1830) being the most abundant. Here we present mitochondrial DNA sequence data from 63 P. verruculata-like specimens to show that they constitute two closely-related clades with distinct sequence signatures and a clear barcode gap. Intraclade distances are 0–1.8% while interclade distances range from 4.7 to 6.0%. Scanning electron microscopy of internal copulation organs reveals that the two clades have distinct penial and accessory gland spine structures, which also differ in size. Using an integrative taxonomic approach, we propose that what was initially thought to be P. verruculata in Singapore, actually are two different species of Peronia.