Phylum Apicomplexa represents one of the most successful groups of eukaryotic unicellular parasites consisting entirely of parasitic genera that infect a wide spectrum of vertebrates and invertebrates. In our research, we focus on early emerging apicomplexans such as protococcidia, agamococcidia, blastogregarines, archigregarines and eugregarines restricted to marine invertebrates. Considering the need for troubleshooting when working with marine parasites from invertebrate hosts, the importance of our work lies in the developing of laboratory protocols that are routinely used for analyses of human pathogens, such as Toxoplasma gondii or Plasmodium spp., but so far not applied to the basal apicomplexans. Results showed that each model organism requires specific conditions for experimental work and processing for further analysis, and hence it was necessary first to set up the protocols for all methodical approaches. We tested the effect of various fixations and prolonged sample storage on preservation of membranes, glycocalyx, and epitopes of protein antigens. We consider as a great success that we are able to stop the motility of model marine apicomplexans isolated from their hosts and kept in vitro, recover them to the normal physiological conditions and maintain them alive for next 24 hours or more. Our methods include field sampling of marine organisms; parasitological dissection and further processing of parasites, squash preparations and parasitized host tissues; light microscopy including imaging and videodocumentation; in vitro experiments; confocal laser scanning microscopy; histology; electron microscopy including the freeze etching; and molecular analysis. Sampling was performed each year (2013, 2014) in the period of 2-3 weeks in the area of the Nikolai Pertsov White Sea Biological Station of the MSU in collaboration with T. G. Simdyanov and G. G. Paskerova. The next part of presentation dealt with the exact results obtained in the years 2012-2014.