Managing the spread and load of pathogen-transmitting ticks is an important task worldwide. The cattletick, Rhipicephalus microplus, not only impacts the economy through losses in dairy and meat pro-duction, but also raises concerns for human health in regards to the potential of certain transmittedpathogens becoming zoonotic. However, novel strategies to control R. microplus are hindered by lack ofunderstanding tick biology and the discovery of suitable vaccine or acaricide targets. The importance oftransmembrane proteins as vaccine targets are well known, as is the case in tick vaccines with Bm86 asantigen. In this study, we describe the localization and functional annotation of 878 putative transmem-brane proteins. Thirty proteins could be confirmed in the R. microplus gut using LC-MS/MS analysis andtheir roles in tick biology are discussed. To the best of our knowledge, 19 targets have not been reportedbefore in any proteomics study in various tick species and the possibility of using the identified proteins astargets for tick control are discussed. Although tissue expression of identified putative proteins throughexpansive proteomics is necessary, this study demonstrates the possibility of using bioinformatics forthe identification of targets for further evaluation in tick control strategies.