Handroanthus impetiginosus, introduced from South America and Central America, had widely used as ornamental tree in southern China, which had rich germplasm resources. However, the resources of introduction is complex while the work of improved variety breeding is lagging. In order to reveal genetic variation of H. impetiginosus populations, the genetic diversity and population genetic structure of 72 samples from 12 populations collected from 6 cities in Guangdong Province were analyzed. The results showed that a total of 123 alleles were amplified by 9 pairs of SSR primers with average PIC of 0.754, indicating that the H. impetiginosus germplasm had high genetic diversity. All 12 populations of H. impetiginosus also had high genetic diversity, the average effective alleles between populations was 3.272, and the average Shannon information index was 1.159. AMOVA analysis showed that genetic differentiation among populations was relatively low, while that within populations was high. The overall genetic differentiation coefficient of populations was 0.077, which was in the medium degree. Based on the Structure analysis, PCoA analysis and NJ clustering analysis, 12 populations of H. impetiginosus could be divided into 2 groups, and the grouping results had certain similarity, indicating that the genetic structure of tested populations was not complex. These would provide a theoretical basis for the utilization of germplasm resources, genetic variation and scientific breeding for H. impetiginosus.