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The visual characteristics of animals with different circadian habits, especially colubrid snakes, exhibit highly variable photoreceptor morphology. While studies have reported on the diversity in retinal cell morphology among snakes with different circadian patterns, few studies have examined the expression of genes related to vision. To explore gene expression patterns in the eyes between diurnal and nocturnal snakes, we carried out RNA sequencing of six tissues (eye, heart, liver, lung, kidney, and muscle) in two colubrids with disparate circadian activities, i.e., diurnal <i>Ahaetulla prasina</i> and nocturnal <i>Lycodon flavozonatum</i>, followed by weighted gene co-expression network analysis (WGCNA). The genes in the two most correlated modules were primarily enriched in different functional pathways, thus suggesting different biological functions. Three opsin genes (<i>RH1</i>, <i>LWS</i>, and <i>SWS</i>) were differentially expressed between the two species. Moreover, in the phototransduction pathway, different genes were highly expressed in the eyes of both species, reflecting specific expression patterns in the eyes of snakes with different circadian activity. We also confirmed the dominance of cone- and rod-related genes in diurnal and nocturnal adaptation, respectively. This work provides an important foundation for genetic research on visual adaptation in snakes and provides further insight into the adaptive evolution of such species.