Abstract
<title>Abstract</title> <p> Blackflies in the genus <italic>Simulium</italic> are the sole vectors of <italic>Onchocerca volvulus</italic> , the human filarial parasite responsible for onchocerciasis (river blindness), a neglected tropical disease endemic to sub-Saharan Africa, the Americas, and Yemen. Species within this genus exhibit significant biological variation, including differences in host and ecological preference, breeding site selection, and vector competence, resulting in varied transmission dynamics across regions. A key challenge in <italic>O. volvulus</italic> vector surveillance is species delimitation within the <italic>Simulium damnosum</italic> complex, due to the lack of distinctive informative morphological markers in adults and consequent reliance on cytotaxonomy, which requires larval stages and is unsuitable for routine use. Here, we present the first nuclear genome assemblies for three <italic>Simulium</italic> species: two assemblies from the <italic>Simulium damnosum</italic> complex and one from the <italic>Simulium neavei</italic> complex, using a hybrid <italic>de novo</italic> assembly approach that integrates Oxford Nanopore and Illumina data. We conducted comparative genomic analyses to annotate orthologous gene clusters and assess genetic divergence. Alignments over tens to hundreds of kilobases revealed a mosaic of syntenic and highly differentiated regions between <italic>S. damnosum s.l.</italic> from East and West Africa. These new genome assemblies will serve as a foundational resource for studying genome evolution and adaptation in these vector species and for a genome-based taxonomy. </p>