Genomics studies face specific challenges in the inner ear due to the multiple types and limited amounts of inner ear cells that are arranged in a very delicate structure. However, advances in single-cell sequencing (SCS) technology have made it possible to analyze gene expression variations across different cell types as well as within specific cell groups that were previously considered to be homogeneous. In this review, we summarize recent advances in inner ear research brought about by the use of SCS that have delineated tissue heterogeneity, identified unknown cell subtypes, discovered novel cell markers, and revealed dynamic signaling pathways during development.