Abstract Inter- and intra-specific compatibility systems in the genus Nicotiana have been used to identify factors that control pollen recognition. N. alata has a classic gametophytic self-incompatibility (SI) system in which the specificity of pollen rejection is determined by a multiallelic S-locus. S-RNases are products of the S-locus, and are the factors that determine specificity in the style. In vitro mutagenesis experiments have been conducted to determine how allelic specificity is encoded in the S-RNase sequence. Plant transformation experiments have shown that S-RNases also act as factors controlling interspecific pollen rejection. By examining the effect of S-RNases on inter- and intra-specific compatibility in different genetic backgrounds, four different pollen rejection mechanisms can be recognized. S-RNases are implicated in three of these mechanisms. The dependence of pollen rejection on genetic background shows that S-RNases interact with other factors. In general, such factors can be classified in three groups based on their mode of interaction with the S-locus and other pollen–pistil interaction pathways. Some of these factors are now cloned. As more factors are cloned and characterized, it is becoming apparent that pollen–pistil interactions that were once thought to be distinct are actually interrelated.