Several factors related to biological characteristics of the Citrus species have hampered the development of new varieties through hybridization. Aspects such as long reproductive cycle, high heterozygosity, sterility, inbreeding depression and juvenility among others, limit the improvement of Citrus by conventional methods, as well as the genetic studies on the species. The early production and a large quantity of fruit, as well as a greater quantity of seeds, is an important characteristics of the candidates varieties for citrus rootstocks. In this sense, the objective of this study was to detect QTL (Quantitative Trait Loci) associated with earliness of fruiting and the number of seeds in a F1 progeny originated from a cross between Rangpur lime (Citrus limonia) and Swingle citrumelo (C. paradisi x P. trifoliata). The linkage analysis conducted through Joinmap 3.0 software using the segregation analysis of 94 hybrids produced a genetic map with 552 DArT and 21 SSR markers. The DArT markers that segregated at 3:1 and SSR markers were used as anchors to integrate the map. The markers were distributed into 9 linkage groups, which spanned a total of 676 cM. The QTL mapping was performed using MapQTL 4.0 software and revealed one QTL associated with earliness of fruiting and two QTLs for seed number. Support: INCT Citros (CNPq, Fapesp and Capes).