Abstract:The 3′-terminal genome of 25 Apple chlorotic leaf spot virus (ACLSV) isolates from sand pear (Pyrus pyrifolia) in Wuhan and Hangzhou, and 2 isolates from peach in Wuhan and Xian were amplified by RT-PCR. The sizes of cloned fragments were 674, 679, 680 and 686 bp, respectively, including partial coat protein (CP) gene and 3′-terminal untranslated region (3′-UTR). Phylogenetic analysis on nucleotide (nt) sequences indicated that ACLSV isolates obtained were clustered into two branches or sub-branches in the sub-group I-1 of the group I. The ACLSV isolate hz-48 from sand pear in Hangzhou showed low identities with the other isolates from China, ranging from 83.5% to 87.5% (nt) and 82.6% to 86.2% (amino acid, aa), and was grouped into a separate sub-branch of sub-group I-1 in the phylogenetic tree. The aa multiple alignment of sequenced partial CP revealed that ACLSV isolates showed high variability at the N-terminal part of CP region overlapped with the MP region and relatively conserved at the C-terminal part, whereas the variation positions were also presented in C-terminal part of CP region from the isolate hz-48 analyzed in this study.