Online modular instruction has gained prominence to motivate students to learn mathematics. The study aimed to determine the effect of the online-modular instruction to Mathematics Achievement of High and Low Math ability group of students. The true experimental design, specifically the Randomized Pre test – Post test Control Group Design, Using Matched Group Subject was adopted. The study was conducted at a State University in the northern Philippines, during the first semester school year 2010 – 2011. The 45 first year students enrolled in College Algebra were the respondents. These students were divided creating two matched groups; one for the controlled and one for the experimental. Students under the controlled group were taught the traditional approach of lecture and chalkboard presentation, while students on the experimental group were exposed to online-modular instruction. The study noted deterioration in the achievement level of the low math ability group exposed to online modular instruction. While it discovered neither improvement nor decline in mathematics achievement on the high math ability group of students. As a result, the experimental methodology in teaching mathematics is not advisable for use to low math ability groups. However, it could be adopted in teaching students with high math ability especially when teachers need to attend other functions and could not attend the class.