The present study sought novel changes to the hamster testicular transcriptome during modulation of fertility by well-characterized photoperiodic stimuli. Transition from long days (LD, 14 h light/day) to short days (SD, 10 h light/day) triggered testicular regression (61% reduction of testis weight, relative to LD) in SD-sensitive (SD-S) hamsters within 16 weeks. After 22 weeks of SD exposure, a third cohort of hamsters became SD-refractory (SD-R), and exhibited testicular recrudescence (137% testis weight gain, relative to SD-S). Partial interrogation of the testicular transcriptome by annealing-control-primer-modified differential display PCR provided several candidates for regulation of testicular functions. Multiple linear regression modeling indicated the best correlation for aquaporin 11 (Aqp11) with changes in testis weight. Correlations were also strongest for Aqp11 with expression levels of reference cDNAs that control spermatogenesis (Hspa2 and Tnp2), steroidogenesis (Cox2, 3βHsd, and Srebp2), sperm motility (Catsper1, Pgk2, and Tnp2), inflammation (Cox2), and apoptosis (Bax and Bcl2). Moreover, siRNA-mediated knockdown of testicular Aqp11 mRNA and protein reduced Hspa2 and Tnp2 mRNA levels, and it increased 3βHsd mRNA levels. It also reduced mRNA levels for Sept12, which is a testis-specific inducer of spermatogenesis. These results suggest a central role for testicular Aqp11 signaling in the coordinate regulation of crucial components of fertility.