In a first part of our pilot study of monogeneans molecules we adopted the NGS techniques in order to get the high quality “monogenean-polyopisthocotylean genome/transcriptome matrix”. In a second part of our study this platform was used for the identification of the monogeneans´ dominant protein molecules followed by their further molecular/biochemical characterization. For this purpose we adopted Eudiplozoon nipponicum as a experimental model species; the representative of blood-feeding monogeneans (family Diplozoidae) of fresh water fishes, the ectoparasite from the gills of Cyprinus carpio. The bioinformatic analyses of genomic sequence data were performed; the first genome assembly of 98 mil of E. nipponicum DNA (3 libraries) sequence reads was done and the calculation of genome size was initiated. Up to now, the low coverage (6%) was reached and therefore the distorted number of bases of whole E. nipponicum genome (400 Gb) was estimated. By adoption of homology searches of RNA 158 753 271 bases/223 887 transcripts the 9757 contigs (>1 kb) were assembled and particular protein molecules in E. nipponicum transcriptome data were identified, e.g. peptidases/inhibitors; 29 contigs of cysteine peptidases (e.g. cathepsin L) and 7 contigs of their inhibitors (e.g. cystatins); 12 contigs of serine peptidases (e.g. cathepsin A) and 7 contigs of their inhibitors (e.g. serpin). Employing biochemical, proteomic and molecular tools, we found that cysteine peptidase activities prevailed in soluble protein extracts and excretory/secretory (E/S) products of E. nipponicum and the major part of activity was related to cathepsin L-like. Mass spectrometry revealed several tryptic peptides in E/S products matching to two translated sequences of cathepsin L genes. The dominance of cysteine peptidases of cathepsin L type in E. nipponicum resembles the situation in, e.g., fasciolid trematodes. The cathepsin L3 was cloned and expressed in both bacterial and yeasts expression systems. The recombinant enzyme was purified on Ni-NTA agarose column and the experiments focused on its molecular/biochemical properties were started.