Ticks are ectoparasites of wild and domestic animals and humans that most notably impact global health by transmitting disease-causing pathogens. While information on the molecular interactions between ticks and pathogens that facilitate pathogen infection, development and transmission is limited, a comprehensive understanding of the tick-pathogen interface would be fundamental toward development of new and novel measures for control of both tick infestations and tick-borne pathogens. Recently, vaccine studies using key tick antigens and characterization of tick gene function by RNA interference (RNAi) have provided new information on genes that impact the tick-pathogen interface. In this review we summarize current research and prospects of tick vaccines and genetic manipulation of ticks targeted to the tick-pathogen interface. The knowledge gained from these collective studies will be fundamental toward understanding of tick-pathogen interactions and for formulation of control methods targeted at both ticks and tick-borne pathogens. Use of these molecular approaches will likely contribute to control measures that will notably reduce tick populations and tick-borne diseases in the future.