Mutations in the gene of connexin 26 (Cx26) are the most common cause of human non‑syndromic hereditary deafness. The pathogenesis of deafness caused by Cx26 remains uncertain. To explore the basic mechanism underlying Cx26 null mutations, ultrastructural changes and a number of marker proteins in the cochlear sensory epithelium of Cx26 conditional knockout mice were observed in the current study. Cochlear specimens were obtained from Cx26 conditional knockout mice (cCx26ko), while wild‑type mice served as controls. Antibodies against the pillar cell marker P75, the supporting cell marker prox1 and hair cell markers myosin 6 and phalloidin were labeled in different cells of the cochlear sensory epithelium of cochlear cryosections. The ultrastructural morphology of cochlear sensory epithelium was observed using transmission electron microscopy. Following the observation of cochlear sensory epithelium cell markers for hair cells and supporting cells, no significant changes were observed at the early stage, while the tunnel of the organ of Corti and Nuel's space was not developed prior to hearing onset in cCx26 knockout mice. Cell death was observed from postnatal day 10 (P10). The only region of surviving cells observed in the cochlea was the Hensen cell region, where microglia‑like cells appeared following P180. Overall, the present study showed an abnormal ultrastructural morphology in the cochlear sensory epithelium in cCx26ko mice. Microglia‑like cells may be involved in the process of cell degeneration in cCx26ko mice.