Abstract: In order to clarify the genetic diversity and evolutionary characteristics of Citrus tatter leaf virus (CTLV), the whole genomes of 41 CTLV isolates from 7 different citrus species were analyzed by genetic diversity and genetic evolution. The results showed that: the base composition of 41 CTLV isolates from different citrus species showed AT bias, the ratio of base transition to transversion was 2.875−5.112, the Pi value of nucleotide diversity was 0.030−0.177, and the Hd value of haplotype diversity was 0.900−1.000. The neutral test values were mostly negative and not significant, indicating that the population has not experienced expansion events. The ratio of non-synonymous mutations to synonymous mutations ranged from 0.059 to 0.754, which was a negative selection. The F_ST value in the analysis of molecular variance (AMOVA) was 0.193, indicating high genetic differentiation between populations, with the variation mainly originating from within populations. The phylogenetic analysis showed that there was no significant host specificity in the clustering of CTLV isolated strains. The study showed that 41 CTLV isolates had high nucleotide and haplotype diversity, with gene mutation and negative selection being the key driving forces of their genetic evolution, while the host plant differences had little effect on the genetic evolution of CTLV.