Sponges are good model organisms for early Metazoan evolution and development because of their early separation from other groups of animals. However, genomic research on sponges is slow because of the scarce availability of genomic information - only one sponge species has had its genome completely sequenced so far. Sponges are also good models for environmental adaptation studies, in which species Eunapius subterraneus is of special interest. E. subterraneus is the only known freshwater stygobiont sponge in the world and it is endemic to karst region of Croatia. Sequencing and assembly of Poriferan genomes is not a trivial task due to the presence of numerous endo- and exosymbiontic microorganisms. Sequencing by Nanopore technology yields long reads with higher error rates in comparison to sequencing technologies of second generation. Hybrid approach to genome assembly uses long third-generation reads for closing gaps and joining contigs assembled from accurate but relatively short second-generation reads. I sequenced the genome of E. subterraneus using Oxford Nanopore Technologies MinION sequencer. I assembled reads sequenced on Illumina and Oxford Nanopore Technologies platforms using hybrid approach and then assesed the quality of assembled genomes. Programs I used for the assembly are based on greedy algorithm and de Bruijn graph method. Using more long third-generation reads resulted in longer contigs. Although I obtained long contigs, my assembly contains many contaminations. Further sequencing is needed in order to complete the genome of E. subterraneus.