Provided are a method and apparatus for analyzing genotype data plotted in a two-dimensional space. The method includes: connecting points representing the genotype data to a predetermined point to form straight lines and obtaining angles between adjacent straight lines; extracting the two largest angles from the obtained angles; and analyzing the plotted genotype data using three groups of the genotype data separated by the two extracted largest angles. According to the present invention, when the experimental results of classifying genotype are to be analyzed, the two largest angles from the angles obtained by connecting straight lines between points representing each of the genotype data and a predetermined point plotted in a two-dimensional space are detected, and three data regions separated by the detected two largest angles are used to analyze the genotype data. Thus, a large amount of the experimental data for classifying the genotype can be analyzed rapidly and conveniently.