Microbiologist average salary is $49,835, median salary is $43,620 with a salary range from $21,840 to $1,348,101.Microbiologist salaries are collected from government agencies and companies. Each salary is associated with a real job position.icrobiologist Salary. Microbiologist average salary is $49,835, median salary is $43,620 with a salary range from $21,840 to $1,348,101. Microbiologist salaries are collected from government agencies and companies.