The infection of dengue virus (DENV) and chikungunya virus (CHIKV) can cause global public health problems, many of which are undifferentiated. Thus, their differential diagnosis is critical to proper patient management. In this study, we present a novel multiplex diagnostic system based on the lateral flow assay (LFA) using ficolin-1 and two-color latex beads labeled with antibodies to detect the dengue virus (DENV) and chikungunya virus (CHIKV) in a single strip. We investigated the binding of ficolin-1, a human innate immune system defense protein, to the viral envelope protein (EP) and developed the LFA system that contains the capturing agent, ficolin-1, which was immobilized on the test line. Our diagnostic system could differentially detect DENV-2 and CHIKV based on the color of the detecting agent in the test line of the strip. The limit of detection (LOD) by naked-eye observation in the multiplex LFA for viral EPs was 25 nM and that for the whole virus was 1 ´ 10⁶ TCID50/mL per strip. Thus, multiplex LFA using ficolin-1 provides a rapid method for simultaneously detecting DENV and CHIKV and can be employed to monitor the status of circulating mosquitoes in a region at risk for DENV and/or CHIKV outbreak.