The field of animal-microorganism interactions has grown tremendously in recent decades as our understanding of how microorganisms influence host health and development has widened from the historical perspective as simply agents of disease. The knowledge gained from studying animal-microorganism interactions can bring about new ways for understanding the biology and ecology of the host of interest. Currently there has been little study of microorganisms associated with echinoderms despite the biological, ecological and economic interests that surround these organisms. Echinoderms are potentially interesting microbial environments due to their comparatively simple digestive systems and feeding habits, the lack of a specialized excretory organ and the influence disease has on population regulation for which there are very few described pathogens. This thesis focuses mostly on asteroids but aims to address three questions. 1) What microorganisms are associated with asteroids, 2) what variables shape the microbiome and 3) What are the potential relationships that can occur between the microorganisms found and the host. The third question cannot be fully addressed with the current data. Nonetheless, each chapter presents hypotheses on this subject in the discussion sections. Chapter 1 begins by examining the commonality and genotypic divergence of circular single-stranded DNA viruses among three echinoderm classes. Chapter 2 investigates the diversity and community composition of prokaryotes among asteroids and factors shaping the asteroid microbiome. The results presented herein provide the most comprehensive survey to date of the microbiome composition of echinoderms which provides an important baseline understanding for future work to elucidate the relationships for this host system.