The partial Mantel analysis is a test statistic that is used to measure the resemblance between two distance matrices after controlling for the effect of the third distance matrix measured over the same objects. The method used in this study is; permute the objects in one of the vectors (or matrices). Association on student’s performance of three faculties (Physical Sciences, Biosciences and Engineering) in Nnamdi Azikiwe University, Awka-Nigeria, was used to illustrate the method, where interest is on estimating the resemblance between two faculties students’ performance while controlling for the effect of the third faculty student performance. From the result obtained in this study, we conclude that there exists a strong negative resemblance between the performance of students in faculty of Physical sciences and faculty of Biosciences while controlling for the effect of student performance of faculty of Engineering for 100,000 permutations and using the Canonical distance which is “method three” in the “dist. quant (distance quantity)” function. R 2.13. 0 programming package was used to run the analysis for 100,000 permutations.