Abstract: Species of Ceiba have high ornamental values and are widely introduced and cultivated in the tropical and subtropical regions in the world. It remains unclear whether the so-called“C. speciosa”is really C. speciosa and whether a single species or multiple species were initially introduced in South China. In this study, nrITS sequencing and ISSR markers were used to characterize 172 accessions ofCeiba cultivated in Guangzhou. Analysis of nrITS sequences revealed that the 172 samples ofCeiba consisted of three species, i.e., C. speciosa ,C. insignis andC. crispiflora , and their interspecific hybrids. By comparing species identification based on nrITS sequence and the corresponding traits, five traits (trunk form, presence or absence of stem thorn, number of petal stripes, color of stamen appendages, and flowering period) showed obvious association with nrITS sequence-based species identification, while four other traits (presence or absence of leaf serration, flower size, petal shape, and color of petal apex) did not. ISSR analysis indicated that these samples could be divided into six clades, and again, the five traits mentioned above showed obvious association with the ISSR clustering results. This study reveals, for the first time, that the so-called“C. speciosa”cultivated in South China in fact includes three species ofCeiba and their interspecific hybrids. Therefore, it is not correct to call all the cultivated plants C. speciosa and their status should be identified with morphological traits and molecular data. The resolution of genetic origins and relationships of these germplasm resources ofCeiba paves the way for breeding program and scientific management.