STONE, D. E., S.-H. OH, E.A. TRIPP (Department of Biology, Duke University, Durham, NC 27708), L. E. RI´OS G. (Oficina Te´cnica en Biodiversidad, Consejo Nacional de Areas Protegidas, 5 av. 6-06, zona 1, Edificio del IPM, 7 mo. nivel, Guatemala, Guatemala), and P. S. MANOS (Department of Biology, Duke University, Durham, NC 27708). Natural history, distribution, phylogenetic relationships, and conservation of Central American black walnuts (Juglans sect. Rhysocaryon). J. Torrey Bot. Soc. 136: 1–25. 2009.— The tree genus Juglans (nogal, walnut) is generally thought of as a north temperate group, but most of the 16 species of black walnuts (Juglans sect. Rhysocaryon) occur in subtropical areas of the New World, spanning Central America, Andean South America, and the Greater Antilles. The two species native to Central America (J. olanchana var. olanchana and J. steyermarkii) and two closely related Mexican taxa (J. olanchana var. standleyi and J. pyriformis) have not been studied thoroughly from a comparative systematic perspective, so here we provide a detailed investigation of their morphology and natural history as a first step towards a broad-based synthesis of J. sect. Rhysocaryon. Fieldwork in Guatemala and Mexico provided the material for germination studies, morphological analyses, and phylogenetic reconstruction using DNA sequences. Juglans steyermarkii was rediscovered in its type locality in Guatemala, and new populations were located during the course of fieldwork. SEM analysis of trichome diversity and density, along with leaflet shape, provided characters to differentiate among five taxa of Juglans in the accompanying key. Staminate flowers and pollen examined for the first time in J. steyermarkii showed close morphological similarities to those of other species of black walnuts. Variation in the pattern of nut-wall sculpture appears to be a promising source of variation; however, adequate capture and quantification of this variation will likely require three-dimensional scanning techniques. There was high variability in percent seed germination of the two Central American species and no observed advantage to leaching, scarification, or a prolonged stratification period. DNA studies included in the exploration of three promising sources of nuclear sequence variation: the ETS and ITS (external and internal transcribed spacer of ribosomal DNA), and the second intron of the LEAFY gene. Combined phylogenetic analysis of these sequences provided a moderately resolved topology containing two major groups of black walnuts and a general correlation between phylogeny and geography. The analyses supported a division between taxa from northern Mexico and the USA, and those from southern Mexico, Guatemala, the West Indies (Greater Antilles), and South America. Observations on the geographic range of Juglans in Mexico and Guatemala indicated a frequent association with coffee plantations, suggesting similar climatic requirements. Our studies of the dispersed and most likely fragmented populations indicate that Juglans may still be found in native plant communities as a canopy tree, although it is much more common to observe populations in cleared areas where the trees were retained as shade for coffee. We are not aware of any major efforts to conserve the native nogal in Central America, though they are sometimes left and/or planted as shade trees in coffee fincas. A study conducted in Mexico suggests that Juglans might be useful in agroforestry efforts to rehabilitate degraded sites. Key words: black walnuts, Central America, conservation, DNA, Guatemala, Juglandaceae, Juglans, natural history, nogal, Mexico, phylogeny.