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Background   Rhodnius montenegrensis  (Triatominae), a potential vector of Chagas disease, was described after  R. robustus -like bugs from southwestern Amazonia. Mitochondrial  cytb  sequence near-identity with sympatric  R. robustus  (genotype II) raised doubts about the taxonomic status of  R. montenegrensis , but comparative studies have reported fairly clear morphological and genetic differences between  R. montenegrensis  and laboratory stocks identified as  R. robustus . Here, we use a transcriptome-based approach to investigate this apparent paradox.    Results  We retrieved publicly-available transcriptome sequence-reads from  R. montenegrensis  and from the  R. robustus  stocks used as the taxonomic benchmark in comparative studies. We (i) aligned transcriptome sequence-reads to mitochondrial ( cytb ) and nuclear (ITS2, D2- 28S  and  AmpG ) query sequences (47 overall) from members of the  R. prolixus – R. robustus  cryptic–species complex and related taxa; (ii) computed breadth- and depth-coverage for the 259 consensus sequences generated by these alignments; and, for each locus, (iii) appraised query sequences and full-breadth-coverage consensus sequences in terms of nucleotide-sequence polymorphism and phylogenetic relations. We found evidence confirming that  R. montenegrensis  and  R. robustus  genotype II are genetically indistinguishable and, hence, implying that they are, in all likelihood, the same species. Furthermore, we found compelling genetic evidence that the benchmark ‘ R. robustus ’ stocks used in  R. montenegrensis  description and in later transcriptome-based comparisons are in fact  R. prolixus , although likely mixed to some degree with  R. robustus  (probably genotype II, a.k.a.  R. montenegrensis ).    Conclusions  We illustrate how public-domain genetic/transcriptomic data can help address challenging issues in disease-vector systematics. In our case-study, taxonomic confusion apparently stemmed from the misinterpretation of sequence-data analyses and misidentification of taxonomic-benchmark stocks. More generally, and together with previous reports of mixed and/or misidentified  Rhodnius  spp. laboratory colonies, our results call into question the conclusions of many studies (on morphology, genetics, physiology, behavior, bionomics or interactions with microorganisms including trypanosomes) based on non-genotyped ‘ R. prolixus ’ or ‘ R. robustus ’ stocks. Correct species identification is a prerequisite for investigating the factors that underlie the physiological, behavioral or ecological differences between primary domestic vectors of Chagas disease, such as  R. prolixus , and their sylvatic, medically less-relevant relatives such as  R. robustus  ( s.l. ) including  R. montenegrensis .    Electronic supplementary material  The online version of this article (10.1186/s13071-019-3558-9) contains supplementary material, which is available to authorized users.

parasites and vectors

Transcriptome-based molecular systematics: Rhodnius montenegrensis (Triatominae) and its position within the Rhodnius prolixus–Rhodnius robustus cryptic–species complex