In various animal species with distinct sexes, sequential hermaphroditism occurs whereby adults change their sex. The role of environmental factors in triggering sex change events is still relatively poorly understood, despite that climate-driven sex-ratio distortion may increase extinction risk. Here, we investigated the effect of seasonal temperature fluctuations on the expression of sex-related genes and sex change in the gonochoristic freshwater cnidarian, brown hydra (Hydra oligactis). Individuals of this species reproduce clonally throughout much of the year but switch to sexual reproduction when temperature decreases in autumn. After sexual reproduction, some individuals can revert back to clonality again. We found that clonal offspring derived from these individuals had a relatively high rate of female-to-male transition. The sexual stage was most differentiated in terms of gene expression, with a large number of genes involved in cellular differentiation and gametogenesis differentially expressed between males and females undergoing gamete production, while asexual individuals belonging to the male and female strain were transcriptomically nearly identical following sexual reproduction. These results show that seasonal environmental changes and associated life stage transitions ‘homogenize’ the gene expression profiles of males and females, ultimately enabling the emergence of alternative sexual phenotypes within strains with an otherwise stable sex.