The genus Capsicum presents a wide genetic variability. The most common way to determine this variability has been based upon morphological descriptors. We studied the genetic divergence among populations of ornamental pepper (Capsicum annuum L.) using two different multivariate techniques: Cluster analysis and canonical discriminant variables. The analyses enabled us to determine the morphological descriptors that contributed most to the genetic divergence. The study was carried out in a greenhouse in the Northeastern Brazil, in two years: 2013 and 2014. The experimental design was the completely randomized design, considering two crossed factors: Population and years. Thirteen populations of ornamental pepper were evaluated based on sixteen plant descriptors, six flower descriptors and ten fruit descriptors; eight F 3 populations, resulting from crossing the accessions 134 (P-9) and 77.1 (P-10), and five additional control populations: P-9, P-10, P-11, P-12 and P-13. There was an agreement between the two multivariate techniques in terms of distance between populations. Fruit descriptors contributed most to the genetic divergence, separating the populations used as control (P-11, P-12 and P-13) from the others. This separation is due to the uniformity of these populations in terms of fruit size and weight.