HIV molecular epidemiology is the use of viral genetic sequence data in a public health setting, and it has the potential to improve public health surveillance and prevention efforts. My research focuses on the use of molecular epidemiology in U.S. public health departments, particularly in New York City. To conduct this research, we developed a tool to construct HIV molecular transmission networks: HIV-TRACE (HIV Transmission Cluster Engine). Using HIV-TRACE, we have investigated the dynamics of these transmission networks to evaluate both their epidemiological significance and their utility in identifying potential targets of HIV intervention and prevention efforts. We have also explored the dynamics of transmitted drug resistance across these networks. Our findings make a strong case for the expanded use of HIV molecular epidemiology in the United States.