Here, we present novel high quality genome assemblies for five invasive tephritid species of agricultural concern: Ceratitis capitata, C. quilicii, C. rosa, Zeugodacus cucurbitae and Bactrocera zonata (read depths between 65 and 78x). Three assemblies (C. capitata, C. quilicii and Z. cucurbitae) were scaffolded with chromosome conformation data and annotated using RNAseq reads. For some species this is the first reference genome available (B. zonata, C. quilicii and C. rosa), for others we have published improved annotated genomes (C. capitata and Z. cucurbitae). Together, the new references provide an important resource to advance research on genetic techniques for population control, develop rapid species identification methods, and explore eco-evolutionary studies.