The Mediterranean ascidian Microcosmus sabatieri is among the conspicuous benthic invertebrates, forming dense populations on moderately inclined cliffs. It is an edible species, commercially harvested at the southern part of the Aegean Sea. Considering that the biology of this species has not been adequately studied, a three-year survey was carried out focusing on population structure, allometric relationships and reproductive status of M. sabatieri stocks in Astypalea Island (Dodecanese, south Aegean). Population density showed insignificant temporal variation and lower values at the steeper station, while the pattern of dispersion was random. All measured biometric characters showed high plasticity, especially those related to siphons. All the examined morphometric relationships follow negative allometry. Ascidian length was a good predictor of biomass, and a strong relation was observed between mantle and tunic characters. Gonad somatic index showed a single spawning season per year, in winter. Length–frequency distribution analysis revealed the presence of one mode of medium sized individuals, implying that M. sabatieri stocks are under moderate fishing pressure in the study area.