Next-generation sequencing methods currently represent a robust tool enabling significant enrichment of our knowledge of biological systems at a level which has not been possible ever before. Unfortunately, the transcriptomic/genomic data on members of Monogenea are still extremely limited. Therefore we adopted the NGS techniques to generate a first high quality transcriptome of a representative of blood-feeding monogeneans - Eudiplozoon nipponicum (Diplozoidae: Heteronchoinea), the ectoparasite from the gills of common carp Cyprinus carpio. Using 454 sequencing technology (GS FLX System, Roche), a total of 324 941 reads were generated (average length 423 bp) and assembled into 6910 contigs. The second transcriptome analysis was performed by the MiSeq System (Illumina). A total of 74 823 255 input read pairs, a total of 142 813 all transcripts (median contig length 367 bp) and a total of 119 136 of genes (median contig length 334 bp) were obtained. Currently, the comprehensive bioinformatic analysis is running - the assemblies are in the process of evaluation and a pipeline for annotation of particular genes is being developed. Special attention was paid to peptidases that could be involved in digestion of host´s blood and other biological processes in E. nipponicum.