The Indian garden lizard, Calotes versicolor, an apparently non-chromosomal sex determination (CSD), non-temperature-dependent sex determination (TSD) species, represents a unique category of reptiles where male hormone-treated embryos emerge as males. The present paper traces the modulation of gene activity in the embryonic gonad following dihydrotestosterone (DHT) administration on day 8 of embryonic development. Expression of CvAR, CvWnt4, CvDmrt1 and CvSox9 genes has been studied in the mesonephros gonadal complex (MGC) 2 and 6 days after the treatment by RT-PCR and real-time qPCR. In the treated (30 µg/egg) embryos (sacrificed 48 h after treatment), CvAR was expressed in almost all the MGCs in contrast to its dimorphic expression in controls. CvWnt4, the autosomal ovary-specific gene, which has only basal level of expression in controls, was further down-regulated in the treated embryos. The dimorphic expression pattern of the male-specific CvSox9 and CvDmrt1 does not deviate from that seen in controls, suggesting that it acts upstream of CvAR. It appears that in C. versicolor, the primary sex determining switch for testis is essentially genetic (CvSox9 and CvDmrt1), but the genetic pathway of ovary differentiation, which is initiated later in development, is flexible enough to be modulated by hormones, as in other TSD and genetic sex determination (GSD) reptiles. One of the mechanisms of this flexibility, it appears, could be silencing of the ovary-inducing genes by the male hormones.