Diverse microorganisms are found in marine environment, displaying various physico-chemical ecosystems which are three dimensional, however, many of which still not identified. Since 1990s, we has been cruise a lot of regions of various marine environments such as coastal areas, deep sea including thermal vent and cold-seep, tropical sea and cold regions like Antarctic and Arctic, and more than 3,000 microorganisms were isolated and preserved. The molecular phylogenetic analysis of the isolates led to some interesting affirmative conclusions. To isolate marine bacteria, collected samples such as sediment, seawater or organisms were spread onto ZoBell 2216e agar plate without or with enrichment in various organic substrates such as starch, skim milk, tributyrin, etc. Colonies showing different morphotypes were selected and analyzed by 16S rRNA gene sequencing to determine taxonomic position. As a result, it was found that app. 10% was not similar to the known bacteria, showing the similarity lower than 96% in 16S rRNA sequence, and assumed as novel genus or species. Majority of isolates were classified into gamma-Proteobacteria (42%), followed by Gram-positive bacteria (37%), alpha-Proteobacteria (14%) and CFB-group (7%). Conclusively, most of novel strains from cold seep were affiliated into gamma-Proteobacteria, and novel isolates from open sea into Gram-positive bacteria and alpha-Proteobacteria while novel CFB-group bacteria were mainly isolated from polar region. Novel isolates from coastal environments evenly belong to the four taxonomic groups with a slightly higher probability of grouping into alpha-Proteobacteria. These results imply that a marine environment provides a special ecosystem preferred by a specific group.