In the present study, using the SRAP markers, we analyzed the interspecific phylogenetic relationship of 22 species of Chinese Hedychium to find out fine mapping population. Using the same technique, maps of two species selected by morphological characters were constructed. Phylogenetic analysis showed that 22 species were grouped into three clusters. The mapping parents selected were in one cluster, with a similarity coefficient of 0.31, which is lower than the mean value of 22 species. Two maps with medium-density were constructed. The maternal parent contained 139 loci and spanned 917.1 cM. These loci were distributed in 18 linkage groups. The paternal parent contained 203 loci and spanned 1386.8 cM, which spread over 23 linkage groups. Unfortunately, the number of loci with a segregation ratio of 3:1 was not sufficient for us to link two maps together. For parental selection, we suggested that the phylogenetic relationship as well as complements of characters should be considered. Moreover, our study showed that two species with similarity around or higher than the mean level tend to produce fine mapping population in Hedychium.