DNA fingerprinting using amplified fragment length polymorphisms (AFLPs) was successfully employed to detect genetic relationships and variability among 90 hop cultivars and breeding lines comprising a collection of the world's hop germplasm. Seven AFLP primer combinations produced a total of 347 fragments of which 151 (43.5%)) were polymorphic. One‐hundred and thirty informative, highly reproducible DNA polymorphisms were used to estimate the genetic similarity (GS) which varied between 1.0 (e.g. ‘Saazer’ vs. ‘Tettnanger’) and 1.17 (‘Columbus’ vs. ‘Tettnanger’, ‘Spalter’ and ‘Saazer’). UPGMA (unweighted pair‐group method with arithmetic averages) clustering revealed two main clusters, reflecting the two main sources of origin and the two main breeding objectives: one cluster of mainly European origin representing the aroma pool and a second cluster associating accessions with European germplasm infiltrated by wild American genes with less aroma quality, but a higher bittering potential. Each main branch was composed of four or three subclusters with subgroups, respectively. Assignment of almost all genotypes in the dendrogram was consistent with the pedigree data as far as they are known. Consequently, AFLPs are shown to be suitable for assessing the genetic variability in hop germplasm and are useful for describing the genetic relationships among cultivars and accessions, which allows phylogenetic questions to be addressed.

A male and female linkage map of hop has been constructed using 224 DNA polymorphisms (106 amplified fragment length polymorphisms (AFLPs), three random amplified polymorphic DNAs (RAPDs), one RAPD‐sequence‐tagged‐site (STS), and three microsatellite (STSs) segregating in an F1 population of the English cultivar ‘Wye Target’‐the German male breeding line ‘85/54/15’. Linkage between these loci was estimated using JOINMAP Version 2.0. The final map for the female parent consisted of 110 loci assigned to eight linkage groups covering a distance of 346.7 cM. For the male map, 57 loci could be mapped on nine linkage groups spanning over 227.4 cM. One of these male linkage groups (Gr09‐M) presumably represents the Y chromosome, since all markers assigned (10 AFLPs, three RAPDs and one STS) were closely linked to the male sex (M). Because of their sex‐specific segregation, 10 doubly heterozygous AFLPs spanning a distance of 18.7 cM could be identified as markers describing the X chromosome, which is part of the male and female map. Three STMSs, which had already proved useful in hop genotyping, could be integrated as codominant locus‐specific markers and thus allowed to produce reliable allelic bridges between the female and male counterparts.