Fludioxonil is a new-generation fungicide widely used for postharvest fruit protection. The aim of this study was to produce hitherto unreported immunoreagents for Fludioxonil analysis by immunoassay. Derivatives of this agrochemical were synthesized with different linker tethering sites. Those functionalized haptens were activated, and the purified active esters were efficiently conjugated to different carrier proteins for immunogen and assay antigen preparation. Antibodies to Fludioxonil were raised in rabbits, and their selectivity and affinity were characterized, revealing the significance of the linker. Those antibodies were evaluated using homologous and heterologous conjugates by direct and indirect competitive ELISA formats. Finally, a pair of immunoreagents was identified showing an IC50 value for Fludioxonil of 5.7 μg/L.