The molecular mechanisms regulating caste determination and reproductive division of labor, the hallmarks of insect societies, are poorly defined. The identification of key genes involved in these developmentally important processes will be essential to gain a better understanding of the mechanisms controlling one of the most impressive examples of polyphenism, the caste structure of eusocial species. Here, we applied representational difference analysis of cDNAs, to study differential gene expression between queens (female neotenics) and workers in the dry wood termite Cryptotermes cynocephalus and identified 13 genes that were highly expressed in queens. In addition, we partially cloned several homologous genes of the related termite species Cryptotermes secundus and compared the expression profiles of 10 homologous genes. In most cases, the preferential expression in female neotenics was not conserved between species, despite the close phylogenetic relationship of both Cryptotermes species. It is possible that these genes are associated with known species-specific differences in caste development modes. Only three genes (Neofem1, 2, and 3) showed a conserved and highly preferential expression in female neotenics, suggesting that their products may play important roles in female reproductives, in particular in controlling caste determination and reproductive division of labor.