Tracking virus infection in plants is useful to assess plant susceptibility or resistance. The recombinant cucumber mosaic virus (CMV) expressing a 2b-fused green fluorescent protein (GFP, 25 kDa) gradually loses (within weeks) the GFP gene in plants. Here, we constructed CMV expressing a flavin-based small fluorescent protein (iLOV, 10 kDa). CMV-iLOV still retains iLOV after 28 dpi in upper leaves of inoculated Nicotiana benthamiana and allows long-term monitoring of its distribution in plants. Using CMV-iLOV, we showed that pot1, a recessive allele for resistance to potyviruses, does not confer CMV resistance in tomato.