The eukaryotic diversity from healthy and diseased Lubomirskia baicalensis and Baikalospongia bacillifera sponges was studied by 454 sequencing approach. The drastic mortality of sponges in Lake Baikal during recent years forces the need of screening pathogens associated with sponges. The project was aimed to search for potential ethiological agent of infection. Five healthy, five diseased sponges of both species and ambient water samples were analysed and significant shift in structure of associated organisms was detected.