This dataset contains information collected between November 2019 and October 2020 on ascidian (sea squirt) diversity and chemodiversity in southwestern Madagascar. Data were gathered from three reef sites located in Toliara Bay (Grand Récif and Sarodrano) and Ranobe Bay (Ifaty). The dataset includes species occurrence records, taxonomic identifications based on morphological and anatomical characteristics, diversity assessments, and results of preliminary phytochemical and antioxidant screenings conducted on selected ascidian species.

The primary objective of the dataset is to improve knowledge of Madagascar’s ascidiofauna, a marine group that remains poorly documented despite its recognized biotechnological and pharmaceutical potential. The data support the characterization of species diversity and provide information on the presence of major bioactive chemical groups in selected species, including alkaloids, quaternary ammonium compounds, anthraquinones, sterols, steroids, and triterpenes.

This dataset is intended to serve as a baseline resource for marine biodiversity research, taxonomy, natural product discovery, marine biotechnology, and conservation planning. It may be useful for researchers studying marine chordates diversity, bioprospecting, chemical ecology, and the potential therapeutic applications of marine organisms in Madagascar and the Western Indian Ocean region.