Gyrodactylus cichlidarum and Cichlidogyrus sclerosus, two monogenean ectoparasite species commonly found on the body surface and gills of Nile tilapia (Oreochromis niloticus) respectively, inflicted considerable economic losses in intensive tilapia farming. In order to explore the immune response of tilapia against these two species of monogeneans, expression patterns of five immune-related genes were studied after singular G. cichlidarum or C. sclerosus infection and their coinfection. The transcription levels of IL-1β were up-regulated in the skin after G. cichlidarum infection, reaching a peak at day 5 PI, and in the gills after C. sclerosus infection (peaking at day 8 PI), with significant elevation only detected in the gills after high-dose C. sclerosus infection. A trend favoring increased gill TNF-α expression at day 8 PI of C. sclerosus infection was statistically significant only in the low-dose infection group. TNF-α expression in the skin did not change significantly after G. cichlidarum infection. TGF-β had extremely up-regulated expressions in the gills at day 8 PI after both high- and low-dose C. sclerosus infections, but its significantly promoted expression in the skin was observed only after infection of high-dose G. cichlidarum. Significantly increased expressions of HSP70 and COX-2 in the skin were detected after high-dose G. cichlidarum infections. In comparison to singular infection with either G. cichlidarum or C. sclerosus, concurrent infection resulted in significantly advanced expression of TGF-β in both skin and gills, and lower expressions at day 8 PI, and similar patterns were observed in the expression of IL-1β and TNF-α in the gills. G. cichlidarum infection on the body surface significantly down-regulated the expressions of TNF-α, TGF-β and COX-2 in the gills. In addition, the intensity of G. cichlidarum was significantly positively correlated with that of C. sclerosus (correlation index 0.922, p = 0.000) at day 2 PI under concurrent infection. These results contribute to the understanding of mucosal immunity of fish against monogenean infection, particularly when two monogenean species infect concurrently.