| Rankings | Journal Title | Publisher | h5-index |
| 1 | Frontiers in Microbiology | Frontiers Media S.A. | 72 |
| 2 | mBio | American Society for Microbiology | 67 |
| 3 | Environmental Microbiology | Wiley-Blackwell | 66 |
| 4 | Frontiers in Cellular and Infection Microbiology | Frontiers Media S.A. | 50 |
| 5 | Microbial Cell Factories | BioMed Central | 46 |
| 6 | BMC Microbiology | BioMed Central | 45 |
| 7 | Microbiome | BioMed Central | 37 |
| 8 | Annals of Clinical Microbiology and Antimicrobials | BioMed Central | 25 |
| 9 | Journal of Microbiology and Biotechnology | Integrated Science Publications | 25 |
| 10 | International Journal of Microbiology | Hindawi Publishing Corporation | 24 |
| 11 | AMB Express | Springer | 24 |
| 12 | MicrobiologyOpen | Wiley | 24 |
| 13 | Journal of Oral Microbiology | Taylor & Francis Group | 23 |
| 14 | Brazilian Journal of Microbiology | Sociedade Brasileira de Microbiologia | 23 |
| 15 | Indian Journal of Medical Microbiology | Medknow Publications | 23 |
| 16 | Archives of Microbiology | Springer Verlag | 22 |
| 17 | African Journal of Microbiology Research | Academic Journals | 21 |
| 18 | Microbial Ecology in Health and Disease | Co-Action Publishing | 20 |
| 19 | Iranian Journal of Microbiology | Tehran University of Medical Sciences | 18 |
| 20 | Jundishapur Journal of Microbiology | Kowsar Publishing | 18 |
| 21 | Journal of Microbiology, Biotechnology and Food Sciences | Slovak University of Agriculture | 15 |
| 22 | new microbes and new infections | Elsevier | 15 |
| 23 | Indian Journal of Pathology and Microbiology | Medknow Publications | 15 |
| 24 | Advances in Microbiology | Scientific Research Publishing | 13 |
| 25 | Journal of Plant Pathology & Microbiology | OMICS International | 12 |
| 26 | British Microbiology Research Journal | ScienceDomain International | 12 |
| 27 | Open Journal of Medical Microbiology | Scientific Research Publishing | 11* |
| 28 | Journal of Microbiology & Biology Education | American Society for Microbiology | 10 |
| 29 | Research Journal of Microbiology | Academic Journals, Inc. | 9 |
| 30 | Journal of Microbiology and Infectious Diseases | Association of Health Investigations | 8 |
| 31 | Journal of Microbiology Research | Scientific & Academic Publishing | 8 |
| 32 | Clinical Microbiology: Open Access | OMICS International | 8 |
| 33 | Indian Journal of Microbiology Research | Integrated Science Publications | 2 |
| 34 | Microbiologia Medica | PAGEPress Publications | 2 |
As per Google Scholar h-Index | Date – 07.03.2019