Breakdown of the pollination barrier of self-incompatibility (SI) in older flowers, a phenomenon known as pseudo-self-compatibility or transient SI, has been described as an advantageous reproductive assurance strategy that allows selfing after opportunities for out-crossing have been exhausted [1-9]. Pseudo-self-compatibility is quite prevalent as a mixed mating strategy in nature, but the underlying molecular mechanisms are not known. We had previously shown that Arabidopsis thaliana exhibits cryptic natural variation for pseudo-self-compatibility, which is uncovered by transformation of different accessions with SI specificity-determining SRK and SCR genes from its self-incompatible sister species A. lyrata[10, 11]. Here, by using this transgenic A. thaliana model, we show that pseudo-self-compatibility is caused by a hypomorphic allele of PUB8, an S-locus-linked gene encoding a previously uncharacterized ARM repeat- and U box-containing protein that regulates SRK transcript levels. This is the first gene underlying pseudo-self-compatibility to be identified and the first report in which cryptic natural variation unveiled by a transgene enabled the cloning of a gene for a complex trait.