This study was carried out on 11 Chinese and 12 Japanese silkworm strains maintained by the Center for the Technological Development of Sericulture (CDTS) germplasm bank, located in Pereira, Colombia. The goals were to determine the genetic population structure of the two groups and the association between molecular markers (AFLPs) and important productivity characters. Group analysis showed the separation of the strains according to their geographic origin. The molecular markers and the productivity characters were correlated by multiple variance analysis. The analysis permitted the identification of molecular markers associated with the cocoon weight or the shell weight separately. Some markers were associated with both characters.