Th e reproductive system of fl owering plants can be highly variable, aff ecting their biology, gene fl ow and genetic variability among populations. Petunia secreta is a rare annual endemic species of Pedra do Segredo, located in the municipality of Caçapava do Sul, state of Rio Grande do Sul, Brazil. Although rare, the species possesses a high level of genetic variability. We investigated the reproductive system of P. secreta, including fruit production and seed germinability, in order to determine if its reproductive system can explain its genetic diversity. We sampled fi ve populations and conducted fi ve greenhouse hand-pollination treatments: 1) autonomous apomixis; 2) self-pollination; 3) hand self-pollination; 4) geitonogamy; and 5) cross-pollination. We analysed a total of 40 plants, 468 fl owers, and 6,500 seeds. Only autonomous apomixis and self-pollination did not produce fruit. No diff erences in fruit weight were observed among pollination treatments (P > 0.05). Seeds of two colours were produced, with no diff erences in germinability. Considering all plants, populations, and treatments, the average germinability was 73 % (range 9 % to 100 %). Th ese results, along with other previous studies, indicate that the reproductive systems of P. secreta, and its large eff ective population size, can explain its high genetic diversity.