Background New Caledonia (NC) and French Polynesia (FP) are areas with high circulation of arboviruses. A large serosurvey among horses from NC and FP was carried out to investigate the seroprevalence of flaviviruses in the horse population. Methods 293 equines were sampled and sera analyzed against flaviviruses using a competitive enzyme-linked immunosorbent assay (cELISA). The positive sera were then confirmed by flavivirus-specific microsphere immunoassay (MIA) and seroneutralization tests. Results This serosurvey highlighted that 16.6% (27/163) and 30.8% (40/130) of horses were positive with cELISA in NC and FP respectively while the MIA technique, targeting only flaviviruses responsible for neuroinvasive infections in horses (i.e. WNV, JEV, and TBEV) showed negative results for more than 83% (56/67) of ELISA-positive animals. Seroneutralization tests with the main flaviviruses circulating in the areas revealed that 6.1% (10/163; confidence interval [95% CI] 2.4%–9.8%) of sera in NC and 7.7% (10/130; 95% CI 4.8%–15.2%) in FP were positive for DENV1 while 4.3% (7/163; 95% CI 1.2%–7.4%) in NC and 15.3% (20/130; 95% CI 9.1%–21.5%) in FP were found positive for ZIKAV. Comparatively, seroprevalence of JEV and WNV flaviviruses were much lower (less than 2%) in the two areas. Conclusion This seroprevalence study in horses’ population shows that horse population can be infected by DEN and ZIKA arboviruses and that these viruses induce seroconversions in horses. The consequences of these infections in horses and the role of horses as amplifier host of these viruses are some questions which deserve complementary investigation.