Miniature inverted-repeat transposable elements (MITEs) are known to contribute to the evolution of plants, but only limited information is available for MITEs in thePrunusgenome. We identified a MITE that has been namedFalling Stones, FaSt. All structural features (349-bp size, 82-bp terminal inverted repeats and 9-bp target site duplications) are consistent with this MITE being a putative member of the Mutator transposase superfamily.FaStshowed a preferential accumulation in the short AT-rich segments of the euchromatin region of the peach genome. DNA sequencing and pollination experiments have been performed to confirm that the nested insertion ofFaStinto theS-haplotype-specific F-boxgene of apricot resulted in the breakdown of self-incompatibility (SI). A bioinformatics-based survey of the knownRosaceaeand other genomes and a newly designed polymerase chain reaction (PCR) assay verified thePrunoideae-specific occurrence ofFaStelements. Phylogenetic analysis suggested a recent activity ofFaStin thePrunusgenome. The occurrence of a nested insertion in the apricot genome further supports the recent activity ofFaStin response to abiotic stress conditions. This study reports on a presumably active non-autonomous Mutator element inPrunusthat exhibits a major indirect genome shaping force through inducing loss-of-function mutation in the SI locus.