XYLEM CYSTEINE PEPTIDASE 1 (XCP1) and XCP2 are key autolytic enzymes in programmed cell death of short-lived tracheary elements in plants. However, the patterns of expression of XCP genes remain to be clarified in long-lived ray parenchyma cells, which survive for several years after the completion of secondary wall formation. We isolated full-length cDNAs that encoded three XCPs (PsgXCP1, PsgXCP2A and PsgXCP2B) of Populus. The deduced amino acid sequences of the XCPs revealed three conserved catalytic residues, namely, cysteine (Cys), histidine (His) and asparagine (Asn), indicating that PsgXCP1, PsgXCP2A and PsgXCP2B might function as papain-like cysteine proteases. Ray parenchyma cells in hybrid poplar remained alive for several years, with continuous expression of XCP genes even after obvious secondary wall thickenings. Levels of expression of XCP genes were lower in the innermost annual ring of sapwood than in one and/or two outer annual rings from beyond the innermost sapwood. This result implies that autolysis of ray parenchyma cells might not be fully explained by dramatically enhanced expression of XCP genes just before their programmed death. In addition, the expression of PtaSND1-A1, PtaVND6-A1 and PtaMYB003 genes was detected in all annual ring in sapwood. Our observations suggest that the expression of genes associated with xylem differentiation such as secondary wall formation and cell death continues for several years in long-lived ray parenchyma cells before their death.