<p> Fruit size is a polygenic trait controlled by multiple genomic regions each with small effect. The complex nature of fruit size regulation makes it challenging to dissect individual genes responsible for phenotypic variation. Though recent advances in high-throughput genome sequencing technology in conjunction with improved statistical and computational methods empowered science to explicitly understand the genetic basis underlying multiple fruit quality traits, much of the work that has been done through classical quantitative trait loci (QTL) approach resulted in reduced resolution and instability when evaluating in different genetic backgrounds and different environments. To increase the precision and improve the stability of QTL analyses and to identify genes controlling fruit size, we performed a set of multiple quantitative and molecular genetic analyses to elucidate the underlying genetic architecture of fruit mass. A total of nine genomic regions associated with fruit mass were identified, two of which are novel to this study; markers Md14_26050918 and Md14_26050904. Detected QTLs explained ~ 42% of the total genetic variation of which ~ 20% is explained by the two novel QTLs. Regions responsible for fruit mass variation appear to be under strong additive and epistatic genetic control. These regions exhibited high stability across-family as well as across-years and showed accurate genomic prediction across-family. Additionally, we identified the apple gene family of putative fw2.2 orthologs, naming them Cell Number Regulators (CNRs) genes (MdCNRs). Three CNRs (MdCNR1-3) showed increased expression at early fruit growth in small-fruited crabapple, associating with reduced relative cell production rate (RCPR), suggesting that alteration in cell number that leads to a subsequent reduction in fruit size is probably due to reduced cell division most likely due to changes in CNRs regulation. Furthermore, our study revealed that reduced fruit size is partially due to the shortened cell expansion period after which cell expansion ceases in the small-fruited crabapple species. Together, these data will advance our understanding of dissecting fruit mass genetic architecture and have high potential to be deployed for marker-assisted selection and further breeding approaches. </p>