We present a genome assembly from an individual male
Opomyza germinationis
(Arthropoda; Insecta; Diptera; Opomyzidae). The assembly contains two haplotypes with total lengths of 315.94 megabases and 151.40 megabases. Most of haplotype 1 (75.22%) is scaffolded into 4 chromosomal pseudomolecules, including the X sex chromosome. Most of haplotype 2 (74.88%) is scaffolded into 3 chromosomal pseudomolecules. The mitochondrial genome has also been assembled, with a length of 15.8 kilobases. This assembly was generated as part of the Darwin Tree of Life project, which produces genomes for eukaryotic species found in Britain and Ireland.