Anadenanthera colubrina var. cebil is an important tree species for its cultural, economic, and medicinal uses in South America. In order to characterize A. colubrina populations, we collected fruits from four different sites (San Bernardo, El Cebilar, Metán and El Gallinato) within the species distribution area in Salta Province, Northwestern Argentina. For this, a total of 75 fruits and seeds per site were collected and described using morphological (fruits size and weight; seed weight and number per fruit) and genetic descriptors (ribosomic DNA extraction and PCR; nucleotide alignment and phylogenetic analysis) with standard protocols. Our results showed that the San Bernardo population had the heaviest fruits and seeds (7.89±0.2g and 0.19±0.002, respectively), and the Cebilar population the lightest (6.25±0.18g and 0.15±0.002g, respectively). Fruits and seeds from Metán and El Gallinato showed similar and intermediate values. The proportion viable (39 to 55%) and aborted (43 to 57%) seeds was different, while the proportion of predated (1.7 to 4.2%) seeds was similar among populations. The genetic analysis showed variability of ITS sequences within the especies, and also when compared with the same Brazilian species. Both, morphologic and genetic descriptors showed a high level of similarity between San Bernardo and Metán, and between El Cebilar and El Gallinato populations. Further studies are needed to assess levels of phenotypic and genetic variability within and between populations of different plant species, since this information is crucial for biodiversity and germplasm long-term conservation. Rev. Biol. Trop. 62 (2): 757-767. Epub 2014 June 01.Key words: biodiversity, germplasm bank, molecular markers, nucleotidic sequence, plant conservation.Anadenanthera colubrina var. cebil (Vell.) Brenan belongs to the Fabaceae/Leguminosae family (Lewis, Schrire, MacKinder, & Lock, 2005), Mimosoideae subfamily. This tree species has economic, medicinal, and cultural applications in South America. It is widely distributed in Brazil, Paraguay, Bolivia and Argentina, where it is found in eleven provinces in the Northeast, Northwest and center, in mountain and transition forests and in Chaco Serrano (Siri Von Reis, 1964). It measures up to 35m in height and can reach 60-80cm in diameter. The wood contains tannins, is hard and resistant to termites and is used in construction and furniture, as poles and for firewood. In popular medicine, it is used to treat respiratory problems and inflammations. It is considered a sacred tree by local cultures. Its seeds have been used for over 3 000 years by shamans in rituals and popular medicine as they contain alkaloids derived from dimethyl tryptamine (Carod-Artal & Vásquez-Cabrera, 2007;Demaio, Karlin, & Medina, 2002;Justiniano & Fredericksen, 1998 Andrade, 2006;Monteiro et al., 2006). This species is categorized as "least concern" with low risk of extinction (IUCN, 2012).The characterization of germplasm collections allows the assessment of the variability of the pr...