The similarity or differences of peroxidase isozymes in rootstocks and scions may influence their graft compatibility. This study was conducted to identify peroxidase isozymes that may be used as markers to predict compatibility between pear (Pyrus communis L.) and various quince (Cydonia oblonga Mill.) clones. 'Bartlett' (BT) and 'Beurre Hardy' (BH) pear cultivars are known to form incompatible and compatible grafts, respectively, with quince rootstocks. The two pear scion cultivars were budded on 'quince A' (QA), 'quince BA-29% and 15 selected quince clones from Turkey. Bark and cambial tissues were taken from nonbudded rootstocks and scions, and 4 cm above and below the graft union for peroxidase isozyme analysis performed by starch gel electrophoresis. Isoperoxidase analyses were also performed on samples from the graft unions collected 12 months after grafting. Many isozyme bands were observed commonly in the two scions; however, one anodal peroxidase A was detected in BH (compatible scion) but not in BT (incompatible scion) samples. This isoperoxidase was also detected in QA, Quince BA-29, and nine of the Turkish quince clones. Another isoperoxidase, band B, was detected in BH but not in BT or any of the rootstocks. However, the compatible (BH/QA) and moderately compatible (BT/BA-29) graft union tissues contained bands A and B whereas incompatible graft union tissues (BT/QA) lacked both. Graft union samples involving BT and five Turkish quince clones (705, 609-2, 702, 804, and 806) had both 'A' and 'B' isoperoxidases while one or both of these bands were absent in nonbudded graft partners. Field observations of 3.5 year-old grafts of BT and Turkish quince clones revealed that the vegetative growth (vigor) of BT scion was significantly greater, when grafted on these five clones, than that in graft combinations with other clones. We suggest that matching of isoperoxidase 'A' in quince rootstocks and BH pear scion may be associated with a compatible graft combination. Additionally, presence of isoperoxidases 'A' and 'B' in the graft union tissues may be used as an indicator to predict a compatible graft between BT and quince rootstocks.