Continuous floral persistence caused by impaired petal abscission and senescence is generally detrimental in crops but beneficial in ornamental species, highlighting the species-specific nature of breeding objectives. Although reduced genetic diversity and underutilization of many identified loci have imposed a profound bottleneck on molecular design breeding, divergent breeding goals across species enable strategic repurposing of genes previously considered detrimental. Here, we demonstrate the cross-species functional repurposing of BLADE-ON-PETIOLE (BOP) genes in floral organ abscission and senescence and reveal the underlying molecular mechanism. Knockout of SlBOP genes resulted in defective petal abscission and delayed senescence, thereby compromising fruit appearance quality in tomato. In contrast, knockout of PhBOP genes in petunia produced non-abscission and delayed senescence of corolla, markedly prolonging floral longevity and enhancing ornamental value. Mechanistically, we show that SlBOP transcriptional cofactors undergo phase separation and interact with the transcription factor TMF FAMILY MEMBER 1 (TFAM1) to form heterotypic biomolecular condensates that control abscission zone (AZ) formation, thereby orchestrating programmed floral organ abscission and senescence. Our findings illustrate that cross-species functional analysis and knowledge transfer can provide a promising strategy to mitigate genetic bottlenecks and expand the toolkit for molecular design breeding.