The Special Issue entitled “Biodiversity of Marine Microbes” aimed at highlighting the significance of marine microbes as primary producers, their participation in complex processes and interactions with both the biotic and the abiotic environment, and their important roles in biogeochemical cycles and ecosystem functioning. The issue includes five research papers, covering the diversity and composition of marine microbial communities representing all three domains of life in various marine environments, including coastal eutrophic areas, ice waters, and lagoons. One paper examined the diversity and succession of bacterial and archaeal communities from coastal waters in mesocosm experiments. The combination of classical tools with novel technological advances offers the opportunity to answer fundamental questions and shed light on the complex and diverse life of marine microbes.