To study the genetic basis of phenotypic changes in floral characters associated with mating system divergence in the yellow monkeyflowers (Mimulus, section Simiolus), all pairwise crosses were conducted between four taxa, of which two were independently evolved inbreeders. The effective number of genetic factors differentiating taxa for each of six characters was estimated from backcross and F2 segregation variances, using a model that incorporates dominance. The number of factors, averaged over taxa pairs, ranged from 5.3 (for stigma-anther separation) to 12.8 (for pistil length). Dominance was slight to moderate for most characters, with a slight bias for inbreeding characteristics to be dominant over outbreeding traits. F2 segregation patterns indicate strong genetic correlations among floral size characters but variable correlation of these characters with flowering time and little correlation with stigma-anther separation. Crosses between the two selfing and two outcrossing taxa did not lead to the recovery of extreme transgressive segregants in the F2. These results suggest that either homologous loci are involved in repeated shifts to selfing or that the likelihood of appearance of novel recombinations is limited by the large number of loci, each with small effect. The implications of these results are discussed in the context of recent models of mating system evolution.