The inner ear sensory epithelium is complex and consists of multiple cell types. Cell type-specific analyses are helpful in defining the regulatory pathways that determine cell fate. In order to define cell type-specific regulatory pathways in inner ear development, we characterized the expression of transmembrane cell surface proteins (CD proteins) in the inner ear. We subsequently identified combinations of markers that could allow for inner ear cell type-specific isolation using flow cytometry. Taking this approach, we were able to not only identify the genetic fingerprint of different cell types in the ear, but also RFX, Zeb1 and miR200b as regulators of cell fate/maturation/survival. We continue to develop new approaches for cell type transcriptome and translatome analysis in the ear, and are actively involved in their dissemination in the field.