There are a few very significant differences between microbiology and molecular biology. 

Microbiology: 

• Is the study of the structure and function of microorganisms such as bacteria, viruses, and fungi, which are the smallest form of life
• Focuses on using information obtained through molecular biology for developing treatments and therapies for diseases 
• Is more field-based
• Uses techniques such as endospore staining, ATP test, indole test, bacterial inhibition assay, agar diffusion test, and CAMP test 

Molecular biology: 

• Is the study of biological activities at molecular level, including the structure and function of molecules that make up living cells, and the biological interactions between various biomolecules such as nucleic acids and proteins
• Focuses on understanding the underlying mechanisms of biological processes
• Is a more laboratory-based
• Uses techniques such as macromolecule bottling and probing, gel electrophoresis, PCR, DNA microarray, and molecular cloning,