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Genetic diversity and genetic integrity were tested for wheat (Triticum aestivum L.) landraces conserved in two gene banks with considerably different germplasm management systems. We identified two sets of 17 wheat accessions derived from identical sources collected in Pakistan, which were later deposited at the National Institute of Agrobiological Sciences, Japan (NIAS) and the Plant Genetic Resources Program, Pakistan (PGRP). Regeneration of the conserved germplasm was infrequent at both gene banks. Amplified fragment length polymorphism (AFLP) profiles did not indicate prominent changes in the banding patterns of the wheat landraces conserved at the two gene banks. No significant differences were observed in allele frequency of the detected loci in comparison to the original collections (materials preserved without regeneration and multiplication), except in one accession at NIAS. We conclude that genetic diversity was conserved at these two gene banks with different management systems. However, among the 161 scored loci, 26 AFLP bands disappeared at the same loci in NIAS and PGRP accessions, four disappeared only in NIAS accessions, and 28 only in PGRP accessions. At one particular locus, the band disappeared in 12 PGRP accessions but not in NIAS accessions. The results indicate that unique selection might occur at PGRP and that regeneration strategies to reduce it will be needed in the future. [ABSTRACT FROM AUTHOR]