In 2014, only 8.7% or 202 out of 2313 Higher Education Institutions (HEIs) in the Philippines were reported to offer a BS Biology degree. An analysis of the microbiology programs of 37 HEIs-respondents in 2016 using questionnaire, augmented by data from websites, and personal interviews revealed that only eight HEIs offer a BS Biology program with a major in microbiology. Only one HEI offers BS Microbiology in the whole country. Together with five others, it produces graduates that are automatically qualified to take the certification examination conducted by the Philippine Academy for Microbiology (PAM). In one HEI, its graduates were deemed unqualified to take the PAM examination as they lack Microbial Ecology, a required course. Two other HEIs can produce graduates that can qualify to take the PAM examination by designing a program that will allow students to take all the required courses from a list of microbiology offerings. Some courses are even offered only as electives. One HEI offers all the necessary courses as electives even as a microbiology major program is non-existent. Only the Basic Microbiology course is common to the BS Biology programs of the 37 HEIs that provided sufficient data for analysis. There are graduate programs in Biology in ten HEIs but only the University of Santo Tomas (UST), University of the Philippines Diliman (UPD) and University of the Philippines Los Baños (UPLB) have MS Microbiology programs. Five HEIs have a doctoral program but only UPLB offers a PhD degree in Microbiology, while UPD has a PhD in Biology program with specialization in Microbiology. Except for 9 of 160 faculty members teaching microbiology in 25 HEIs that provided their faculty profile, all have PhD or MS degrees. The establishment of microbiology education consortia in various regions in the country is considered as the most feasible strategy to increase the number of BS Biology graduates who can qualify to become certified microbiologists.