In model systems of homomorphic self-incompatibility (SI), the S-locus constitutes an extensive genomic region comprising a number of expressed loci, including those controlling female (pistil) and male (pollen) function. Most plants are hermaphroditic and recombination suppression, a common feature of mating type regions, consigns the male and female components of SI to a common evolutionary fate. Nevertheless, empirical and theoretical studies of SI have revealed evidence of sexual antagonism over the level of expression of SI. Virtually every system subjected to close examination has now been found to depart from canonical SI. Here, we consider the effects on genetic variation in the vicinity of the S-locus of some non-canonical forms of SI. Partial asexual reproduction tends to reduce the number of S-alleles, while maintaining the extraordinary genealogical depth typical of S-allele lineages. Cycles of partial disablement and restoration of pollen-pistil recognition may have occurred in the history of SI systems of ancient origin.