Expression profile of the brain (ventral part of telenchephalon, hypothalamus and pituitary) of medaka (Oryzias latipes) kept under constant photoperiodic conditions were obtained by RNA-seq analysis. Monthly transcriptomes under constant photoperiodic conditions identified 518 circannual genes. Overall design: To investigated the expression profile of each gene under constant photoperiodic conditions, samples were collected every month and RNA-seq analysis was performed using these time-series samples.