Biliary tract cancers (BTC), which include cholangiocarcinoma (both intra- and extrahepatic) and gallbladder, represent a heterogeneous group of malignancies with relatively low-incidence and poor prognosis. Therapeutic options for BTC patients at advanced stage are severely limited and palliative chemotherapy remains the maintreatment option. In the past decade, genome profiling via next-generation sequencing of large international cohorts has paved the way for precision oncology in BTC, identifying unique molecular subtypes, recurrent mutations, and genomic rearrangements. Targeted therapies directed against some of these aberrations are currently under investigation in phase 3 clinical studies and hold great promise to improve the prognosis of this disease. Thus, in the near term, the individual molecular alterations of the disease rather than the anatomic location will likely drive the design of clinical trials. In this review, we summarize recent molecular discoveries in BTC with a special emphasis on the most promising therapeutic targets, ultimately providing an update on current and future directions in the management of this disease.