Urothelial carcinoma exhibits a wide spectrum of morphologic and molecular heterogeneity. Advances in molecular testing have improved our understanding of the molecular biology of urothelial carcinoma, including recurrent genomic alterations and transcriptomic features, leading to the development of molecular classification schemes with potential therapeutic implications. This review summarizes the molecular characteristics of urothelial carcinoma, focusing on genomic and transcriptomic features, updates on variant histology, and novel biomarkers that may guide contemporary and future clinical management.