ABSTRACT:Inherited retinal degeneration (IRD) is a debilitating condition characterized by progressive loss of photoreceptor cells. However, the underlying mechanisms remain largely unclear. This study investigated the role of DNA topoisomerase II alpha (TOP2A) and its interplay with protein kinase G (PKG) and histone deacetylase (HDAC) in the rd1 mouse model for IRD. Immunofluorescence and quantitative western blotting analyses were performed to evaluate the expression of TOP2A, PKG1, PKG2, HDAC1, and other related markers. TSC24 and suberoylanilide hydroxamic acid were used to specifically inhibit TOP2A and HDAC, respectively, in organotypic retinal explant cultures derived from wild‐type or rd1 mice. Furthermore, we examined the effect of PKG activity on TOP2A phosphorylation using KT5823. Significant upregulation of TOP2A was observed in the rd1 mouse retina compared with wild‐type controls, especially in the outer nuclear layer. Phosphorylation levels of TOP2A strongly correlated with photoreceptor cell death. Treatment with TSC24 significantly reduced TOP2A‐positive and TUNEL‐positive cells. TOP2A phosphorylation was accompanied by HDAC activation, which was mitigated by TSC24. PKG inhibition by KT5823 reduced TOP2A phosphorylation at specific residues and photoreceptor HDAC activity. Our findings position TOP2A in the PKG‐TOP2A‐HDAC photoreceptor degenerative pathway, offering new potential therapeutic targets for combating IRD‐type diseases.image