ABSTRACT In the second half of 20th century the awareness of importance of landraces for the future, led to organized collecting missions for numerous plant species. A total of 2217 maize (Zea mays L.) landraces, collected in the former Yugoslavia, are stored at Maize Research Institute (MRIZP) gene bank. During 2014, new collecting missions were organized in the eastern and western parts of Macedonia. According to collecting site and kernel type, 14 samples from the Faculty of Agricultural Sciences and Food, R. Macedonia were chosen for the comparison and identification of possible duplicates, through coupling with the 16 MRIZP gene bank accessions from the same area and kernel characteristics. Phenotypic characterization was done for 21 traits according to International Board for Plant Genetic Resources descriptors for maize. The Principal Component Analysis (PCA) identifies five PCs with Eigenvalue > 1, explaining 80% of the total phenotypic variation. The most discriminative traits with the strongest positive associations were tasseling and silking dates, plant height, leaf length and ear length. Compared to the ex-situ populations, the number of alleles and the number of specific alleles, showed a significant decrease in the in situ populations. Twelve unique alleles were detected in samples from MRIZP gene bank, and only four were found in new Macedonian samples. Cluster analysis of morphological and molecular markers distinguished groups of maize accessions with distinctive morphological traits and genetic profiles that will be useful for conservation, and management of gene bank collection, as well as for possible utilization in breeding.