Ceiba species have high ornamental value and are widely cultivated in tropical regions. However, genetic background of cultivated Ceiba plants remains unclear. To understand the genetic relatedness of cultivated Ceiba plants and genetic basis of key horticultural traits, here we explored the genetic relatedness of 153 accessions of Ceiba plants cultivated in southern China and identified SNPs associated with five horticultural traits, based on 11 704 SNPs derived from double-digest restriction-site associated DNA sequencing (ddRAD-seq). Clustering analysis revealed that these accessions were composed of three groups: C. speciosa group, C. insignis group, and hybrid group. The GWAS identified two, four, two, three, and four SNPs related to petal color, petal striation number, flowering time, trunk shape, and prickles on the trunk and branches, respectively. One to two candidate genes were found near the SNPs strongly associated with these traits. This study revealed the genetic relatedness in the Ceiba plants cultivated in southern China and presented the first GWAS analysis for five horticultural traits for them, laying a foundation for phenotype-related marker selection and molecular breeding.