Ectoparasitic flatworms from the group Monogenea represent serious fish pathogens. Their presence in stocks can lead to significant losses in fish host populations. Despite this fact, the running research has been focused mainly on morphological and phylogenetical characteristics of these worms and the information related to the biochemical and molecular nature of the physiological processes is rather sporadic. Up to now, we performed whole-genomic sequencing of selected monogenean representative Eudiplozoon nipponicum by three sequencing techniques. 454/Roche (Junior sequencing platform), Illumina (MiSeq and HiSeq sequencing platforms) and recently by Oxford Nanopore (MinION sequencing platform). Using 454/Roche Junior and both Illumina sequencing platforms, 164,773,962 short genomic reads were originally generated. After quality processing of raw reads (trimming, removing contaminants, errors correction, etc.), 130,741,241 reads were used for the draft of genome assembly. Finally, 524,914 contigs were generated by MaSuRCA assembler in total length 1,109,208,298 base pairs (1.1 Gb). Unfortunately, the final assembly was fragmented and significant number of contigs was identified as a bacterial contamination. In order to improve E. nipponicum draft genome, especially to fill the missing genome gaps, we generated long reads using modern third generation sequencing method nanopore sequencing (MinION). The MinION platform (Oxford Nanopore Technologies, UK) is a small and portable, real time working, low-cost USB device, producing very long-reads (theoretically up to 250 Kb). The results of our analysis with E. nipponicum DNA showed, that 500 active channels/pores (from max. 512) produced 1,091,445 reads with length up to 198,101 base pairs (average 2,588 base pairs). In total, more than 2,8 Gb were generated in two days run, it significantly helped us to improve genome information by merging a relevant percentage of contigs (9.7 %), from 524,914 to 474,134.