Sweet cherry (Prunus avium L.) is a rosaceous fruit crop cultivated in temperate regions of the world for its highly valued fruits. In today’s marketplace, large fruit is highly desirable and directly related to grower profitability; therefore, the development of new cherry varieties with large fruit is a major breeding goal. To elucidate the genetic control of fruit size in sweet cherry and thereby enable marker‐assisted breeding, we undertook a fine mapping – candidate gene analysis of two previously identified fruit size QTLs located on linkage groups 2 and 6 (G2 and G6)(Zhang et al. 2010) in two sweet cherry populations. A total of 14 simple sequence repeats were developed from the peach genomic regions syntenic to the G2 and G6 fruit size QTLs and used to further narrow the sweet cherry QTL regions. Genome annotations of the peach sequence in these syntenic regions identified cell number regulator genes (CNR, Guo et al. 2010) as likely candidate genes for both the G2 and G6 fruit size QTLs. The CNR gene family, first described in maize based upon homology to the tomato fruit weight gene fw2.2, is hypothesized to contain genes involved in cell number regulation that ultimately affect plant growth and organ size. Sequencing of the CNR candidate genes from the parents of the mapping populations and a panel of diverse sweet cherry selections for G2 and G6 identified 3 and 2 allelic variants, respectively. These findings agree with the previously described functional haplotypes for these two fruit size QTLs. Comparisons of sweet cherry fruit weights based on their CNR genotypes further support our hypothesis that the phenotypic differences in fruit size associated with the G2 and G6 QTLs are caused by allelic variants of the CNR genes.