Seeds from species of Canarium L. (Burseraceae) have been recommended as a potential nut crop for global trade that, if adopted, would be the first 'new' nut commodity since the introduction of the Macadamia nut in the early 20th century. The present study addresses several knowledge gaps about the evolutionary biology of Canarium species in order to explore their phylogeny and cultivation history in greater detail. The phylogeny of select Canarium species (16 spp.) from the three taxonomic sections of the genus was reconstructed using DNA sequence data from seven regions and included cultivated species C. album (Lour.) Raeusch., C. decumanum Gaertn., C. harveyi Seem., C. indicum L., C. ovatum Engl., C. tramdenum C.D. Dai et Yakovlev, and C. vulgare Leenh.. Sequence data from the nuclear genome (rDNA external transcribed spacer (ETS), the third intron of nitrate reductase (NIA-i3)) and the chloroplast genome (rbcL, rps16 intron, psbA-trnH spacer, trnL intron and trnL-F spacer) were analyzed using parsimony and Bayesian inference. Results indicate that Canarium comprises at least two distantly related evolutionary lineages within its tribe, desirable fruit characteristics of cultivated and wild-harvested edible species have evolved multiple times, and autopolyploidization rather than allopolyploidization may have been associated with speciation in Canarium sensu stricto. The markers ETS, NIA-i3, rps16 intron, and psbAtrnH spacer will provide the most informative variation for future expanded studies of Canarium phylogeny, although detailed morphological study and taxonomic revision of the genus will be necessary as well.