This is a hard question to answer given the fact that the current and future scopes of both the fields are terrific. Biotechnology deals with merging technology with biolpgical systems. Microbiology is more related to the lifecycles of the microbes. This is a research oriented field wherras Biotechnology involvesmodifying products or processes for specific use. Now the salaries depend on the area of opportunities. Biotechnolpgy graduates can study MBA and move to Managerial positions while Microbiology more of being research oriented, has oppirtunities in research fields. Now when compared, research oppprtunities pay less than the Managerial positions. Having said that, MBA has no specific subject criteira and so if a Microbiology graduate wants to do MBA, he/she can and improve the pay scale. But if the student wants to confine himself/herself to research, Biotechnology pays a little higher.