Neoleucinodes elegantalis (Guenée) is an oligophagous species of plants in the Solanaceae family that has a broad geographical distribution in the tropical zones of South America. It is the most important insect pest of naranjilla (Solanum quitoense Lamarck), a crop grown in threatened areas of the tropical old-growth forest in Ecuador. In this study, two host-specific populations of N. elegantalis were collected from infested fruit of naranjilla and tree tomato (Solanum betaceum Cavanilles) in different locations. Sexually virgin adult insects (93 females and 103 males) were dissected to extract their genitalia to measure 12 morphological variables in females and six in males, resulting in six and four informative variables respectively. Using univariate and multivariate analysis of variance, it was found that the Solanaceous host was the main factor differentiating the area measurements of the seventh abdominal segment and ostium bursae in female genitalia, and cornuti length in male genitalia. Principal components generated with these measurements were employed in a logistic regression model for the classification of the Solanaceous host. Female genitalia of individuals from S. betaceum showed significantly larger ostium bursae relative to female genitalia from S. quitoense. For males, individuals collected from S. betaceum showed longer cornuti length than samples collected from S. quitoense. The results suggest genotypic differentiation according to the Solanaceous host or phenotypic plasticity in N. elegantalis. Further molecular and bio-geographical studies are needed to properly differentiate N. elegantalis populations that would help in the control of this pest.