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Abstract Phlebotomine sand flies are the vectors of leishmaniasis, a neglected tropical disease. High-quality reference genomes are an important tool for understanding the biology and eco-evolutionary dynamics underpinning disease epidemiology. Previous leishmaniasis vector reference sequences were limited by sequencing technologies available at the time and inadequate for high-resolution genomic inquiry. Here, we present updated reference assemblies of two sand flies,Phlebotomus papatasiandLutzomyia longipalpis. These chromosome-level assemblies were generated using an ultra-low input library protocol, PacBio HiFi long reads, and Hi-C technology. The newP. papatasireference has a final assembly span of 351.6 Mb and contig and scaffold N50s of 926 kb and 111.8 Mb, respectively. The newLu. longipalpisreference has a final assembly span of 147.8 Mb and contig and scaffold N50s of 1.09 Mb and 40.6 Mb, respectively. Benchmarking Universal Single-Copy Orthologue (BUSCO) assessments indicated 94.5% and 95.6% complete single copy insecta orthologs forP. papatasiandLu. longipalpis. These improved assemblies will serve as an invaluable resource for future genomic work on phlebotomine sandflies.