A review of valid species within genus Pygmaeconus Puillandre & Tenorio, 2017, is presented. Combined analysis of molecular [partial mitochondrial cytochrome c oxidase subunit I (cox1) gene sequences of several individuals, and a nearly-complete mitogenome for one individual] and morphological (shell and radular tooth) characters revealed that tiny cone snails collected with algae and shell grit by scuba at 12 m depth in the southeastern Philippines correspond to a new species, introduced here under the name Pygmaeconus atomus sp. nov. It attains a maximum adult size of < 5 mm, being arguably the smallest recorded member of the cone-snail fauna worldwide.