Due to advances in molecular biology and the unfolding of new information, many microorganisms have been renamed.
Here is the list of some of these microorganisms with their former and new name.
| New Name | Formerly known as |
| Cystoisospora belli | Isospora belli |
| Klebsiella aerogenes | Enterobacter aerogenes |
| Clostridioides difficile | Clostridium difficile |
| Burkholderia cepacia | Pseudomonas cepacia |
| Prevotella melaninogenica | Bacteroides melaninogenicus |
| Anaplasma phagocytophilum | Ehrlichia equi |
| Burkholderia pseudomallei | Pseudomonas pseudomallei |
| Chryseobacterium | Flavobacterium |
| Stenotrophomonas maltophilia | Pseudomonas maltophilia |
| Prevotella melaninogenica | Bacteroides melaninogenicus |
| Pneumocystis jirovecii | Pneumocystis carinii |
| Rhizopus arrhizus | Rhizopus oryzae |
