A new species belonging to the recently described genus Malagodon Meinema and Huber, 2023, is herein described from specimens collected in a single, small, isolated Pandanas swamp in southeastern coastal Madagascar, located within the Réserve Spéciale de Manombo, south of the town of Farafangana, its only known locality. The new species was last collected in the late 1990s, and despite repeated attempts over the past three decades, no additional specimens have been collected at the type locality or from any other suitable habitats within the region, and the species is presumed to be extinct. The new species is distinguished from its only congener, Malagodon madagascariensis, formerly known from forested swamps in northeastern coastal Madagascar, and also now considered to be extinct, by the following apomorphic features: a lower anal-fin ray count (15–17 vs. 18–19), a longer caudal peduncle (26.8%–39.8% vs. 21.9%–26.7% SL), and the presence of a platelike (vs. thin and spinelike) neural spine on the fifth vertebral centrum in both sexes. Additionally, the new species exhibits neural spines on both the sixth and seventh vertebral centra that are also somewhat expanded and platelike dorsally compared with those in M. madagascariensis, which are narrow and spinelike. We also provide a rediagnosis of Malagodon based on the examination of additional material unavailable in the original description, which was based on only three specimens (two males of M. madagascariensis and one female of the new species).