Research on the human and animal inner ear remains challenging due to its small size and its location within the temporal bone. Recent cellular and molecular biology methods, originally developed for brain and retina neuroscience, have been applied to understand the cellular and molecular biology of the inner ear. In this collection, we present current methods for investigating the anatomy and cellular and molecular biology of the human and animal inner ear, including 3D reconstruction, 3D imaging, immunohistochemical techniques, artificial intelligence 3D imaging models, and various omics approaches (DNA and RNA sequencing). These methodologies are beginning to decipher the intricate organization of the inner ear in humans and various animal models. They will enable the development of better strategies to prevent hearing loss and the creation of cell-based animal models for hearing recovery research.