The competence of plants to shed organs in response to developmental or environmental signals is remarkably variable. Species including cotton abscise flowers, leaves and young fruits throughout their life cycles. Arabidopsis, in contrast, sheds floral parts but neither leaves nor pods. Our long-term goal is to understand the molecular basis of cell separation during abscission, including aspects not shared between organs. Here, we identify ethylene-dependent and independent processes required for cell separation within abscission zones (AZs) of crop and model plants. In cotton (Gossypium hirsutum), transgenic studies provide evidence for mechanistically distinct processes controlling leaf and flower bud shed. Antisense suppression of ACC oxidase-mediated ethylene biosynthesis significantly suppresses leaf, but not flower bud abscission in transgenic plants subjected to water stress and rehydration. Sequencing of cDNA libraries constructed from abscission zones of equivalently stressed wildtype organs provides evidence that abscission in different organs is accompanied by expression of different gene populations. Ethylene synthesis may not control abscission in all organs and/or may depend upon different enzymes in different settings. A more comprehensive assessment of ethylene-dependent and independent abscission processes was conducted in Arabidopsis flower parts shedding after pollination. A developmental series of stamen AZs was isolated by laser capture microdissection and used to prepare hybridization targets for whole genome profiling. Gene chip studies coupled with functional analyses of highly regulated genes in genetically modified plants suggest that ethylene-dependent and independent routes running in parallel contribute to successful organ detachment.