Tomoto aspermy virus (TAV) and Chrysanthemum virus B (CVB) were detected after samples of chrysanthemum showing noticeable symptom of virus diseaseas were collected at flower bases and parks in Kunming in 2011. On the basis of ELISA test and RT-PCR detection, the resulted incidences of the TAV and CVB were 4.62% and 16.70% respectively. Partial coat protein (CP) gene in 3 isolates of TAV and 8 isolates of CVB were sequeced. The sequencing results indicate the homology between the 3 TAV isolates in Kunming and other 28 accessed isolates in GenBank is 85.04%-98.02%. These isolates were built up in two clusters in the phylogenetic tree, and the TAV isolates in Kunming were built up in the same cluster. However,a comparison between the 8 isolates of CVB in Kunming and the other known 35 isolates in GenBank indicates their homology is 75.09%-84.99%. These isolates were built up in three clusters in the phylogenetic tree, and the CVB isolates in Kunming were built up in the same cluster.