Abstract The Galápagos Islands are home to incredible endemic biodiversity that is of high conservation interest. Two such endemic species are the Galápagos tomatoes: Solanum cheesmaniae and Solanum galapagense . Both are known from historical location records, but like many endemic plant species on the Galápagos, their current conservation status is unclear. We revisited previously documented sites of endemic species on San Cristóbal, Santa Cruz, and Isabela, and document the disappearance of >80% of these populations. In contrast, we find that two invasive relatives ( Solanum pimpinellifolium and Solanum lycopersicum ) are now highly abundant, and in some cases—based on morphological observations—might be hybridizing with endemics. Our findings suggest that expanding human developments and putative interspecific hybridization are among the major factors affecting the prevalence of invasives and the threatened persistence of the endemic populations.