The genome duplication and chromosome rearrangement are two kinds of evolution models at the chromosome level during the evolution of vertebrate genome. And Hox genes are the powerful proves to support the evolution theory of genome duplication, which has been found recently. In this study, the chromosomal localization of rice field eel Hox genes has been carried out by PRINS. The mapping results indicated that 6 Hox clusters might exist in rice field eel genome, and these clusters were localized on chromosome 1, 2, 3, 6, 8, 10 and at the position of 28.24 +/- 2.88, 4.55 +/- 1.39, 13.89 +/- 2.03, 74.32 +/- 1.86, 38.03 +/- 2.41, 58.18 +/- 2.05 from the centromere respectively. The mapping results that Hox genes were localized on chromosome 1, 3, 6 and 10 in the study are corresponding to that by chromosome microdissection. The chromosomal localization of rice field eel Hox genes will help us to discover the origin and evolution of rice field eel chromosomes, and provide cellular genetic proves of this special species to support the evolution theory of genome duplication.