Aging-associated functional decline is accompanied by alterations in the epigenome. To explore DNA modifications that could influence visual function with age, we perform whole-genome bisulfite sequencing of purified mouse rod photoreceptors at four ages and identify 2,054 differentially methylated regions (DMRs). We detect many DMRs during early stages of aging and in rod regulatory regions, and some of these cluster at chromosomal hotspots, especially on chromosome 10, which includes a longevity interactome. Integration of methylome to age-related transcriptome changes, chromatin signatures, and first-order protein-protein interactions uncover an enrichment of DMRs in altered pathways that are associated with rod function, aging, and energy metabolism. In concordance, we detect reduced basal mitochondrial respiration and increased fatty acid dependency with retinal age in ex vivo assays. Our study reveals age-dependent genomic and chromatin features susceptible to DNA methylation changes in rod photoreceptors and identifies a link between DNA methylation and energy metabolism in aging. Display omitted •WGBS identifies 2,054 differentially methylated regions (DMRs) in aging mouse rods•DMRs are present in regulatory regions and cluster at chromosomal hotspots•DMRs are linked to dysregulation of aging pathways and energy metabolism•Old retinas exhibit lower basal respiration and higher fatty acid dependency The crosstalk between chromatin modifications and aging hallmarks is poorly understood, especially in neurons. Using purified rod photoreceptors, Corso-Díaz et al. identify aging-associated differentially DNA methylated regions that greatly overlap regulatory elements and are linked to lower mitochondrial basal respiration and higher fatty acid dependency.