Polygalacturonases (PGs) have been proposed to play an important role in the process of cell separation. The Arabidopsis thaliana genome contains 69 annotated genes that by amino acid homology and transcript organization could be classified as putative PGs and these can be grouped into multiple clades. An analysis of five members located in two separate clades, using reporter fusion constructs and reverse transcription-PCR, revealed that whilst these PGs exhibit high sequence similarity they have distinct patterns of spatial and temporal expression. Sites of expression include the aleurone and endosperm cells surrounding the emerging radicle in a germinating seed, the cortical cells adjacent to the developing lateral root, the abscission zones of floral organs, the dehiscence zone of anthers and siliques, and pollen grains. Silencing of an abscission-related PG (At2g41850), using a T-DNA insertion strategy, delayed the time-course of floral organ loss but did not prevent shedding from taking place. These observations are discussed with regard to the contribution that PGs may play during the life cycle of a plant.