This work evaluated the occurrence and genetic structure of Rhodnius nasutus sampled in two sites using morphometry and microsatellites. These sites, presented distinct abiotic features and palm trees: (i) nine Attalea speciosa palm trees, so called babaçu, were sampled from the Meruoca Mountain Ridge, a sloping region of reminiscent forest in the state of Ceará, Brazil, and (ii) 17 Copernicia prunifera palm trees, so called carnaúba, were sampled in the scrub savanna region (Sobral district) that surrounds the mountain ridge. Of the twenty-six palm trees dissected, 70.6% of carnauba and 88.9% of babaçu were infested by R. nasutus. The micro-climatic data where R. nasutus were sheltered demonstrated that the babaçu and carnaúba palm trees presented significant differences (p < 0.05) in relation to the external environment, except for temperature and relative humidity regulation, suggesting that the architecture of the babaçu crown keeps a more stable micro-environment. The morphometric studies of the F1 generation demonstrated that insects from the babaçu (A. speciosa) were significantly larger (p = 0.000) than those collected in carnaúba (C. prunifera) palm trees. Also, microsatellite analysis demonstrated a high genetic differentiation between the two groups of R. nasutus (Rst = −0.77). Our results suggest that the difference in size between the populations is probably related to an incipient process of genetic drift in populations associated to each palm tree, probably also driven by the different climatic features observed in these micro-environments.