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Dengue viruses are some of the most important mosquito-borne pathogens worldwide. They cause illness in 50–100 million individuals per year and have a significant global health impact in low- and middle-income countries. It is important to improve our understanding of the humoral response to dengue virus, as antibodies (Abs) are associated with protection from or susceptibility to severe dengue disease. In recent years, significant advances have been made toward identifying Ab targets and evaluating the functional properties of Abs. However, much less is known about the cellular source of Abs, B cells, in part because the reagents to phenotype and characterize antigen-specific B cells have been challenging to develop. Here, we discuss our recent experience with developing and using fluorescent viruses to probe the B cell response to dengue virus. We present the strengths and weaknesses of flow cytometric analysis of antigen-specific B cells and discuss the use of these probes to phenotype and characterize specific B cells during and after natural infection and in ongoing dengue vaccine trials.