Abstract: This paper focused on the variation and phylogeny relationship of four microsatellite loci originated from maire yew（Taxus chinensis var. mairei）. Comparison of allelic size and sequences indicated that abundant variation and complex SSR structure existed in four SSR loci. Inter-allelic size variation in SSR loci was due to the mutation of SSR repeats and insertions or deletions（Indels） in flanking regions，which also the main reason caused the allelic size mismatch with sequences data. Two sets allelic homoplasy were observed in TY05 locus where alleles identical in state are not identical by descent. Mitochondrial DNA heteroplasmy was detected in one mitochondrial SSR locus（TB01）. Allelic distribution and their phylogeny relationship suggested that stepwise mutation model（SMM）appropriated for these loci，common allele have the characteristic of aboriginality on evolution phylogeny.

Key words: Taxus chinensis var. mairei, microsatellite marker, allele, sequence variation, gene mutation