Homeobox genes encode transcription factors controlling development; however, a number of homeobox genes are expressed postnatally specifically in melatonin-producing pinealocytes of the pineal gland and photoreceptors of the retina along with transcripts devoted to melatonin synthesis and phototransduction. Homeobox genes regulate melatonin synthesis in pinealocytes, but some homeobox genes also seem to be involved in regulation of retinal phototransduction. Due to the lack of photoreceptor models, we here introduce the rat pinealocyte culture as an in vitro model for studying retinal phototransduction. Systematic qPCR analyses were performed on the rat retina and pineal gland in 24 hour in vivo series and on primary cultures of rat pinealocytes: All homeobox genes and melatonin synthesis components, as well as nine out of ten phototransduction genes, were readily detectable in all three experimental settings, confirming molecular similarity between cultured pinealocytes and in vivo retinal tissue. 24 hours circadian expression was mostly confined to transcripts in the pineal gland, including a novel rhythm in arrestin (Sag). Individual knockdown of the homeobox genes orthodenticle homeobox 2 (Otx2), cone-rod homeobox (Crx) and LIM homeobox 4 (Lhx4) in pinealocyte culture using siRNA resulted in specific downregulation of transcripts representing all levels of phototransduction; thus, all phototransduction genes studied in culture were affected by one or several siRNA treatments. Histological colocalization of homeobox and phototransduction transcripts in the rat retinal photoreceptor was confirmed by RNAscope in situ hybridization, thus suggesting that homeobox gene-encoded transcription factors control postnatal expression of phototransduction genes in the retinal photoreceptor.