Melon yellow spot virus (MYSV), a member of the genus Tospovirus, is a devastating thrips-transmitted virus of cucurbits. The cucumber accession 27028930 was found to be resistant to MYSV in our previous study. In the present study, we identified quantitative trait loci (QTLs) conferring resistance to two MYSV isolates, MYSV-FuCu05P and MYSV-S. An F-2 population derived from a cross between accession 27028930 and the susceptible cultivar 'Tokiwa' was used to test for MYSV-FuCu05P resistance and to construct a genetic linkage map. The map contains 7 linkage groups and is comprised of 81 simple sequence repeat (SSR) markers, which span 715 cM, with an average interval between markers of 9.7 cM. Two major QTLs [on chromosomes (Chr.) 1 and 3] and one minor QTL (Chr. 7) contributed by 27028930, and one minor QTL (Chr. 4) contributed by 'Tokiwa' were detected for MYSV-FuCu05P resistance. Another F-2 population from the same cross was used to test for MYSV-S resistance and to construct a genetic linkage map. The latter map also contains 7 linkage groups and is comprised of 76 SSR markers, which span 674 cM with an average interval between markers of 9.8 cM. A resistance gene for MYSV-S was identified on Chr. 3 by linkage analysis. Using independent populations, we demonstrated that SSR markers linked to the major QTLs for MYSV-FuCu05P resistance on Chr. 1 and 3 and an SSR marker linked to a resistance gene for MYSV-S on Chr. 3 could be used to select for MYSV resistance in cucumber breeding.