This is normal, because you have only two groups. Refer to Canonical Structure , if you have K groups, K-1 canonical variables are obtained. In the situation of two groups, there is just 1 canonical variable. You can see how the coordinates are defined by going to the platform red triangle menu, select Canonical Options > Save Canonical Scores, to save the values to the original data table. In addition, for your example, the two groups are well separable.