In the present study, we used high-throughput sequencing to capture and enrich exonic regions. With the help of the BaitFisher software, we developed a new bait kit (SYRPHIDAE1.0) to target 1945 CDS regions belonging to 1312 orthologous genes. This new bait kit was successfully used to exon-capture the targeted loci in 121 flower fly species across the different syrphid subfamilies. We analyzed different amino acid and nucleotide data sets with the Maximum Likelihood and the Multispecies Coalescent approaches. Our analyses yielded highly supported similar topologies, although the degree of the SRH (global Stationarity, Reversibility and Homogeneity) conditions varied greatly between amino acid and nucleotide data sets. The sisterhood of subfamilies Pipizinae and Syrphinae is recovered in all our analyses, confirming a common origin of taxa feeding on soft-bodied arthropods. Based on our results, we redefine the tribe Syrphini stat.rev. and infer the origin of the Syrphidae using BEAST.