Ectoparasitic flatworms from the family Diplozoidae (Platyhelminthes, Monogenea) represent a serious bloodfeeding fish pathogens. Until now, 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. To this date only two monogenean genomes are deposited in public sequence databases. Genomes of Gyrodactylus salaris (Monopisthocotylea, Gyrodactylidae) and Protopolystoma xenopodis (Polyopisthocotylea, Polystomatidae). Therefore, we designed whole-genomic sequencing of selected monogenean representative - Eudiplozoon nipponicum Goto 1891, which was performed by three sequencing techniques. 454/Roche (Junior sequencing platform), Illumina (MiSeq and HiSeq sequencing platforms) and modern Oxford Nanopore technique (MinION sequencing platform). Using 454/Roche Junior and both Illumina sequencing platforms, 164,773,962 short raw reads were originally generated. After trimming of low quality reads (Trimmomatic v. 0.36) and removing contaminatinon - reads given by fish host (Cyprinus carpio), 130,741,241 reads were used for the draft of genome assembly. Finally, 766,162 scaffolds were generated in total length 1,322,576,402 base pairs (1.3 Gb). But most of assembled scaffolds were identified as a Spiroplasma sp. or Emticicia oligotrophica (bacterial contaminations), which could mean that significant number of E. nipponicum reads could be unintentionally filtered out and final scaffold is incomplete. For purpose to improve E. nipponicum genome draft, we have additionally included reads generated by modern third generation sequencing method – nanopore sequencing. The MinION platform is a small and portable, real time working, low-cost USB device, producing long-read (theoretically up to 250 Kb). 500 working channels produced 1,097,634 reads with length up to 198,101 base pairs.