Although morphological plasticity has been widely known in various cactus genera, few studies have investigated the origin and molecular relationship between morphological variants from cacti. Morphological variants are relevant specimens because atypical, exotic and generally unique forms are preferred by cactus traders and collectors. The current study investigates the molecular relationship between the tortuosus and monstruosus ornamental variants of Cereus peruvianus used in landscapes. Polymorphisms in loci of simple-sequence repeats in DNA were used as molecular markers. The variants tortuosus and monstruosus, and plants with typically columnar and erect shoots cultivated in southern Brazil were retrieved from public parks and home gardens. High polymorphism, an indicative of vegetative propagation, and a moderate genetic divergence were detected at the molecular level in monstruosus and tortuosus plants. Artificial selection and vegetative propagation of the ornamental variants of Cereus may be inducing a moderate genetic divergence and formation of two heterologous groups with conservative genetic diversity. Polymorphism in Cereus variants revealed groups with contrasting genes among the variants tortuosus and monstruosus which may be useful for breeding to generate new and different new variants.