The Myristicaceae, or nutmeg family, consists of 21 genera and about 500 species of dioecious canopy to sub canopy trees that are distributed worldwide in tropical rainforests. The Myristicaceae are of considerable ecological and ethnobotanical significance as they are important food for many animals and are harvested by humans for timber, spices, dart/arrow poison, medicine, and a hallucinogenic snuff employed in medico-religious ceremonies. Despite the importance of the Myristicaceae throughout the wet tropics, our taxonomic knowledge of these trees is primarily based on the last revision of the five neotropical genera completed in 1937. The objective of this thesis was to perform a molecular and morphological study of the neotropical genera Compsoneura and Virola. To this end, I generated phylogenetic hypotheses, surveyed morphological and genetic diversity of focal species, and tested the ability of DNA barcodes to distinguish species of wild nutmegs. Morphological and molecular analyses of Compsoneura. indicate a deep divergence between two monophyletic clades corresponding to informal sections Hadrocarpa and Compsoneura. Although 23 loci were tested for DNA variability, only the trnH-psbA intergenic spacer contained enough variation to delimit 11 of 13 species sequenced. A morphological and molecular investigation of Compsoneura capitellata showed little discrete morphological variation among populations but significant genetic structure among populations. Phylogenetic analysis of Virola also revealed a deep molecular divergence between two clades having numerous contrasting morphologies. In contrast to Compsoneura, the trnH-psbA intergenic spacer failed to differentiate the majority of Virola species tested. An infraspecific morphological and molecular study of V. sebifera and V. loretensis showed that each of these species contains morphologically and ecologically discrete sympatric morphotypes that likely represent new species. In total, this investigation found 5 provisional new species from fewer than 600 collections at biological stations in Ecuador and Peru where these new species were among the most abundant trees in the forest. This suggests that much diversity likely remains to be described in the Myristicaceae and other tropical plant families.