Ocotea quixos (Lam.) Kosterm. (Ishpingo) is a tree that grows in humid tropical forests in South America (310-1200 masl). It is used for food and medicine, since it possesses essential oils with antiplatelet and antithrombotic properties, among others. In Ecuador, the wild populations of Ishpingo have been reduced ecosystem transformation, deforestation and clonal cultivation. This study compared the genetic variability of three regions of chloroplast DNA (i.e., matK, rbcLa and psbA-trnH) and one nuclear region (i.e., ITS) in Ishpingo from 5 provinces of the Ecuadorian Amazon. Based on the obtained alignments, the phylogeny was performed by using the maximum likelihood criterion with a bootstrap of 1000 replicates and with the Jukes-Cantor correction. The genetic variability was determined using the DNA conservation coefficient and the Nei (π) nucleotide variability coefficient. The nucleotide variability of matK, rbcLa and psbA-trnH regions was low (π ≤ 0.005) due to their high conservation degrees. The ITS region presented a superior variability (π = 0.11) by grouping the samples that were analyzed into two clades. The regions that were analyzed were not useful for the study of genetic variability in Ishpingo. Therefore, it is recommended that new chloroplast and nuclear DNA regions be analyzed to allow studies on the population genetics of this species in Ecuador to be carried out.