The phylogeny of Rutaceae subfamily Aurantioideae has previously been estimated only using plastid and repetitive nuclear sequences. We added sequences of two low copy nuclear loci to allow further diagnosis of phenomena that may mislead phylogenetic inference. After testing for patterns expected under recombination, positive selection, and hybridization, we excluded data sets or sequences accordingly and then inferred the species tree using the multispecies coalescent. We then reconstructed the ancestral area using parsimony and the dispersal-extinction-cladogenesis model to test the hypothesis that Citrus s. l. may have originated in Australasia and migrated or rafted to Eastern Asia. The ancestral area of Citrus s. l. inferred under either method and several models was west of Wallace's line. Therefore, Citrus s. l. did not appear to have rafted west on what became the Halmahera Islands (Indonesia). Our findings are also consistent with previously reported ages for the origin of this group that may be too young to have allowed this rafting. The species tree is well resolved and largely consistent with previous molecular phylogenies, especially those using chloroplast sequences.