Abstract: Based on the emerging field of molecular systematics as a powerful classification tool，a
phylogenetic analysis was conducted using sequences of the Internal Transcribed Spacer of nuclear
ribosomal DNA（rDNA ITS）as DNA bar-codes for phylogenetic analysis of Capsicum plants. Seventeen
pepper（Capsicum）resources were collected from different localities and sequenced ITS for all samples by
sanger dideoxy method. Furthermore，other ITS sequences of Solanum lycopersicum（Shanghai906），C.
baccatum，C. pubescens，C. frutescens，C. eximium and C. lycianthoides were downloaded from GenBank
and aligned with the sequences obtained in this study by Clustalx 2 software. Then，the（G + C）content，
divergence and similarity among sequences were analyzed by DNAstar software. Finally，based on the ITS
sequences，phylogenetic tree was reconstructed by MEGA5.1 software using Solanum lycopersicon
（Shanghai 906）as an outgroup to root the tree. The alignment result indicated a 15-base deletion in the
ITS1 region for C. chinense（No. 6，7，8），C. pubescens（No. 20）and C. frutescens（No. 22）but not in C. annuum，C. baccatum，C. eximium and C. lycianthoides. According to the analysis of phylogeny，the 22
Capsicum samples were divided into 6 clustered，all of C. annuum samples were clustered together. C.
chinense and C. frutescens were clustered together. The result indicated that the genetic relationships of C.
chinense and C. frutescens were close. C. eximium，C. baccatum，C. pubescens and C. lycianthoides
represent entirely different branches.

Key words: Capsicum, ITS sequence, phylogenetic analysis