The fungus Aspergillus niger is an industrial producer of pectin degrading enzymes. The recent solving of the genomic sequence of A. niger allowed an inventory of the entire genome of the fungus for potential carbohydrate degrading enzymes. By applying bioinformatics tools 12 new genes putatively encoding family 28 glycoside hydrolases were identified. Seven of the newly discovered genes form a new gene group, which we show to encode exo-acting pectinolytic glycoside hydrolases. This group includes four exo-polygalacturonan hydrolases (PGAX, PGXA, PGXB and PGXC) and three putative exo-rhamnogalacturonan hydrolases (RGXA, RGXB and RGXC). Biochemical identification using polygalacturonic acid and xylogalacturonan as substrates demonstrated that indeed PGXB and PGXC act as exopolygalacturonases while PGXA acts as an exo-xylogalacturonan hydrolase. The expression levels of all 21 genes were assessed by microarray analysis. The results from this study demonstrate that exo-acting glycoside hydrolases play a prominent role in pectin degradation.