To cope with seasonal environmental changes, animals adapt their physiology and behavior in response to photoperiod. However, the molecular mechanisms underlying these adaptive changes are not completely understood. Japanese medaka fish (Oryzias latipes) serve as an excellent model to study the mechanism of seasonal adaptation, because of their highly sophisticated seasonal responses and the recent availability of genomic information and genome-editing tools. We show using genome-wide expression analysis of the brain that an uncharacterized long non-coding RNA (lncRNA), LDAIR, is strongly regulated by photoperiod in medaka fish. Numerous transcripts and signaling pathways are activated during the transition from short day (SD) to long day (LD) conditions, but LDAIR is one of the first genes to be induced, and its expression shows a robust daily rhythm in LD. Transcriptome analysis of LDAIR knockout (KO) fish reveals that the LDAIR locus regulates a gene neighborhood, including corticotropin releasing hormone receptor 2 (CRHR2), which is involved in the stress response. Behavioral analysis of LDAIR KO fish demonstrates that LDAIR affects self-protective behaviors under LD conditions. We therefore propose that photoperiodic regulation of CRHR2 by LDAIR modulates adaptive behaviors to seasonal environmental changes.