Microbial eukaryotes are quantitatively predominant, highly diverse and functionally important groups of eukaryotes in the deep oceans. Investigations on the microbial eukaryotic diversity provide not only the base for elucidating the structure of deepsea ecosystems but also high support for better understanding the microbial diversity and their geographic distribution. So far, the biodiversity research on microbial eukaryotes obviously lags behind that of prokaryotes. Our knowledge of their morphological diversity mainly comes from groups (e.g. foraminiferans) that need not cultivate and are easily identified with external morphology. The application of molecular methods greatly extended our knowledge of the microbial eukaryotic diversity in deep sea, uncovering a much higher molecular than morphological diversity. More and more undescribed taxa and even novel evolutionary lineages of eukaryotes have been discovered from deep sea. By reviewing and summarizing literature data, the authors present the research progress and existing problems in the biodiversity of microbial eukaryotes in deep sea, and propose possible solutions and key issues for future research.