The genus Artocarpus J.R. Forster & G. Forster shows a higher diversity along the tropics of Indo Malayan region to Australasia. The Artocarpus phylogeny is resolved in previous studies. According to morpho-genetic assessments, Artocarpus spp. have been subdivided into subgenera and sections. However, the published phylogenies did not comprise the Artocarpus spp. found in Sri Lanka, leaving an ambiguity of their phylogenetic positions. The morphology was observed in many trees in natural range, and the line diagrams were drawn to showcase the morphological features that can be used to classify the Artocarpus spp. into subgenera and sections. We collected leaf samples from the Artocarpus spp. in Sri Lanka. The genomic DNA was extracted, and PCR amplified for five markers (trnH-psbA, rbcL, trnL-F spacer, trnSGCU-trnGUUC, and ITS1-4) followed by sequencing. The Artocarpus phylogeny was constructed in Maximum Likelihood and Bayesian framework using the generated sequences and the related sequence-popsets. Moreover, a divergence dating analysis was also carried out to check the evolutionary history of Sri Lankan Artocarpus spp. According to the morphology and phylogeny, the subgeneric classification of A. heterophyllus Lam, A. altilis (Parkinson) Fosberg, and, A. camansi Blanco was in line with previous studies. The dating analysis revealed a recent introduction of A. heterophyllus, A. altilis, and, A. camansi into Sri Lanka because of the associated food values. We positioned A. nobilis Thwaites, an endemic species to Sri Lanka, in the Artocarpus phylogeny under section Duricarpus. The nomenclatural status of A. gomezianus Wall. Ex Trecul coming under subspecies zeylanicus was verified as it does not clade closely with true A. gomezianus. However, we kept the species name as A. gomezianus as both true A. gomezianus, and Sri Lankan species got 10–13 pairs of lateral veins and the whitish hair underneath the leaf. We also recognized three ancient lineages of subgenera Artocarpus and Pseudojaca. These species naturally occur in India and Sri Lanka where they might be close descendants of the common ancestors of the subgenera Artocarpus and Pseudojaca.