Rhodnius pallescens is the principal vector of Chagas disease in Panama. Recently a dark chromatic morph has been discovered in the highlands of Veraguas Province. Limited genetic studies have been conducted with regards to the population structure and dispersal potential of Triatominae vectors, particularly in R. pallescens. Next generation sequencing methods such as RADseq and complete mitochondrial DNA (mtDNA) genome sequencing have great potential for examining vector biology across space and time. Here we utilize a RADseq method (3RAD), along with complete mtDNA sequencing, to examine the population structure of the two chromatic morpho types of R. pallescens in Panama. We sequenced 105 R. pallescens samples from five localities in Panama. We generated a 2216 SNP dataset and 6 complete mtDNA genomes. RADseq showed significant differentiation among the five localities (FCT = 0.695; P = .004), but most of this was between localities with the dark vs. light chromatic morphs (Veraguas vs. Panama Oeste). The mtDNA genomes showed a 97–98% similarity between dark and light chromatic morphs across all genes and a 502 bp insert in light morphs. Thus, both the RADseq and mtDNA data showed highly differentiated clades with essentially no gene flow between the dark and light chromatic morphs from Veraguas and central Panama respectively. We discuss the growing evidence showing clear distinctions between these two morpho types with the possibility that these are separate species, an area of research that requires further investigation. Finally, we discuss the cost-effectiveness of 3RAD which is a third of the cost compared to other RADseq methods used recently in Chagas disease vector research.