ABSTRACT There are endemic cacti species in the North of Chile with edible fruits and a fledgling productive potential, with unknown degree diversity. Low diversity compromises the ability of populations to evolve and reduces their chances of survival under environmental changes. Copao (Eulychnia acida Phil.), a cactus endemic to Chile that grows in the Coquimbo Region (30° S lat) and able to bear fruit in water stress conditions, were morphologically characterized using descriptors of other columnar cacti at three different locations where it usually grows wild. Five inter simple sequence repeat (ISSR) primers, which were reported for other cacti that produced replicable and informative amplifications, were selected for the genetic characterization. Statistical analysis was performed to describe the diversity of this species and morphological and genetic results compared each other. High variation was observed between and within the evaluated populations for parameters of central tendency, dispersion, and univariate statistical analysis of the morphological traits. Principal component analysis showed that 73% of the population variation at the three locations could be explained by the first three principal components with 34%, 22%, and 17% of the observed variation, respectively. The five ISSR primers generated 7 to 11 polymorphic bands with a band range between 100 and 1517 bp. The polymorphic information content (PIC) averaged 0.75, which suggests high diversity between and within populations. Consensus of 85% existed between the selected descriptors and the ISSR markers, which points them out as suitable tools to analyze diversity in this species.