Embryos produced in vivo and in vitro show morphological and developmental differences, which can be related to culture environment. Nevertheless, there are a few studies showing the effect of in vitro environment on embryos from different bovine subspecies, such as Gyr (Bos indicus) and Holstein (Bos taurus). The aim of this study was to evaluate the relative abundance of aquaporin 3 (AQP3) and ATPase-α1 (Na/K-ATPase alpha 1) transcripts in blastocysts produced in vivo or in vitro from Gyr and Holstein cattle. The production system effect (in vivo × in vitro) for Gyr cattle and the breed effect (Holstein × Gyr) for in vitro-produced embryos were evaluated. For each group, blastocysts (n = 15) distributed in 3 pools were used for RNA extraction (RNeasy MicroKit, Qiagen, Valencia, CA), followed by RNA amplification (Messageamp II amplification kit, Ambion-Applied Biosystems, Foster City, CA) and reverse transcription (SuperScript III First-Stand Synthesis Supermix, Invitrogen, Carlsbad, CA). The cDNA obtained were submitted to real-time PCR, using the H2a gene as endogenous control, and analyzed with REST software^© using the pair wise fixed reallocation randomization Test. There was no difference (P > 0.05) in gene expression for AQP3 and ATPase-α1 between in vivo- and in vitro-produced Gyr embryos, although the results suggest that the APQ3 gene was down-regulated (0.81 ± 0.31) and the ATPase-α1 gene was up-regulated (1.20 ± 0.65) in embryos produced in vitro. For breed effect within in vitro production system, ATPase-α1 gene was down-regulated in Holstein (0.56 ± 0.30) when compared with Gyr embryos (P < 0.05). The same trend was observed for AQP3 (0.58 ± 0.25), but with no difference (P > 0.05). In conclusion, the data suggest that embryo production system does not interfere with the transcript amount of the genes studied for Gyr cattle; however, the in vitro production system may have different effects on gene expression according to embryo breed. Other genes should be evaluated for a better understanding of these differences.