Three varieties of the introduced Bidens pilosa (Hairy beggar-ticks; Asteraceae) co-exist in Taiwan. Bidens pilosa var. minor and var. pilosa are naturalised, while only var. radiata is invasive. Differences in seed set in bagged versus open-pollinated capitula, pollen–pistil interactions and the pollen/ovule (P/O) ratio were investigated among these three varieties. In contrast with the resulting 45–55% seed set in each bagged capitulum of var. minor and var. pilosa, almost no mature seeds (1–2 seeds) were found in bagged capitula of var. radiata, showing that var. radiata has a low capability of autonomous seed production. In bagged capitula, only 1.5% of pistils of var. radiata, but 76% and 52% of those of var. minor and pilosa, respectively, had pollen tubes penetrating into their styles, suggesting that var. radiata has strong self-incompatibility mechanisms preventing autonomous autogamy. The P/O ratio, with mean values of 8189, 2053 and 1613 for var. radiata, var. minor and var. pilosa, respectively, were counted. These results support the hypothesis that the three varieties bear different breeding systems; the invasive var. radiata is highly self-incompatible, whereas the other two naturalised varieties are self-compatible.