This checklist of Malagasy Cucurbitaceae comprises 26 genera with 77 species and five varieties, including five new species to be formally described when more complete ecological and genetic data are available. Of the 82 taxa, 65 are classified as indigenous, and of those, 52 species and 5 varieties are endemic (88% of the native taxa). Six exotic species have permanent populations outside cultivation (naturalised exotics). Another eleven exotics are cultivated and occasionally found escaped from cultivation (casuals). The checklist covers taxonomic information including type specimen(s), vernacular names, DNA sequence information, photos, global and national distribution data with status (endemic, non-endemic native, naturalised, or cultivated), plus ecological and habitat information. Our analysis of IUCN conservation status suggests that half of the native species (32) are threatened, mainly due to habitat destruction. For 12 taxa we lack information to suggest IUCN status but many of them might turn out to be threatened or even extinct. Nine species are absent from protected area, 21 were found only in a single reserve. The Andohahela National Park is home to the greatest Cucurbitaceae diversity with 13 species, followed by Zombitsy-Vohibasia with 12 species. The most species-rich genera are Peponium (up to ten endemic species), Zehneria (eight species, six of them endemic), Ampelosycios and Xerosicyos (each seven endemic species). Our study reveals overlooked diversity in a plant family of global importance and highlights the need for additional fieldwork and collection in several genera, including Cayaponia, Cyclantheropsis, Peponium, and Kedrostis.