We present a genome assembly from an individual male Eustalomyia histrio (Anthomyiid fly; Arthropoda; Insecta; Diptera; Anthomyiidae). The genome sequence is 871.3 megabases in span. Most of the assembly is scaffolded into 6 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 19.42 kilobases in length. Gene annotation of this assembly on Ensembl identified 26,785 protein coding genes.