We present a haploid genome assembly from an individual Lichina pygmaea (Black Lichen; Ascomycota; Lichinomycetes; Lichinales; Lichinaceae). The genome sequence has a total length of 32.42 megabases. The assembly is scaffolded into 7 chromosomal pseudomolecules. The mitochondrial genome has also been assembled, with a length of 47.95 kilobases. Gene annotation of this assembly on Ensembl identified 8 665 protein-coding genes. From the metagenome data, we recovered 9 bins, of which 4 were high-quality MAGs. Keywords: Lichina pygmaea; Black Lichen; genome sequence; chromosomal; Lichinales.