The family Trypanosomatidae comprises obligate parasites of invertebrates, mainly insects, of plants and of all classes of vertebrates including man. Trypanosomatids exclusive of insects have been reported in more than 400 species worldwide, mostly of dipterans and hemipterans. Insect trypanosomatids were distributed in the genera Crithidia, Blastocrithidia, Leptomonas, Herpetomonas and Wallaceina. These genera have not been corroborated by phylogenetic studies and broader analyses are required for a contemporary appraisal of the Taxonomy of insect trypanosomatids. Our main goals were to revise the taxonomy of the genus Herpetomonas and of Symbiont Harboring Trypanosomatids (SHTs), which are common parasites of dipterans. For this purpose, during our study we compared ~130 trypanosomatids from flies captured in South America (Brazil, Venezuela and Colombia) and Africa (Mozambique, Guinea Bissau and Madagascar). We compared the barcodes (V7V8 SSU rRNA sequences) of 4 reference species and 9 new SHTs to assess the genetic diversity and to select isolates for inclusion in phylogenetic trees. The resulting phylogenies (SSU rRNA and gGAPDH) supported the monophyly of the SHT and its partition in two subclades corresponding to the genera Strigomonas and Angomonas revalidated in this study; these genera were distantly related to Blastocrithidia, Herpetomonas and Crithidia. Morphological and phylogenetic data enabled the description of Angomonas comprising 10 flagellates including A. deanei and A. desouzai plus the new A. ambiguus, and Strigomonas including S. oncopelti, S. culicis and the new S. galati. Analyses of 16SrRNA and ITS1rDNA revealed three new species of trypanosomatid proteobacterial endosymbionts (TPEs), and the partial congruence of SHT and TPE phylogenies support a co-divergent host-symbiont evolutionary history for most species excepting for A. ambiguus. Barcoding of 364 cultures from flies collected in South America and Africa identified 70 cultures (20%) as Angomonas, 50 (71%) of them from blowflies (Calliphoridae). Surveys by PCR directly of 13 fly guts revealed that ~50% of the blowflies were infected by Angomonas. Of the 83 samples, 70 from cultures and 13 uncultivated, 61 were A. deanei, 16 A. desouzai and 6 A. ambiguus. Phylogenetic analysis (gGAPDH) of SHTs corroborated the existence of 3 main clades leaded by A. deanei, A. desouzai and A. ambiguus, and disclosed cryptic intra-specific diversity represented by four genotypes of A. deanei and two of A. desouzai. The phylogeny of the SHTs and TPEs were congruent. Four genotypes of A. deanei and "Ca. K. crithidii" and two genotypes of A. desouzai and "Ca. K. desouzaii" corroborated the SHT-TPE co-divergence. A. deanei and A. ambiguus shared the same TPE. The partial congruence between SHTs and TPEs suggests a predominant clonal propagation with sporadic recombination. Chrysomya and Lucilia (Calliphoridae) yielded 73% of the isolates followed by Muscidae with 14%. Despite the strong Angomonas-blowflies association, these flies are also common hosts o...