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Hierarchical and nonhierarchical clustering methods are used for classifying genetic resources. In hierarchical clustering methods, all variables (categorical and continuous) can be used to form the subpopolations (groups or clusters), but in standard nonhierarchical methods only the continuous variables are incorporated in the analysis. The Location model (LM) allows classifying individuals into homogeneous subpopulations by continuous and categorical variables. In practice, the multinomial variable of the LM that arises from the combination of all the categorical variables usually shows empty cells in some subpopulations with the consequence of not allowing estimation of cell means and within‐cell variances and covariances. The main objectives of this study were (i) to develop the Modified Location model (MLM) that allows empty cells in some subpopulations under the assumption that the means and the …