Technical Abstract: Linkage mapping and genetic diversity studies with randomly amplified polymorphic DNA (RAPD) or amplified fragment length polymorphisms (AFLP) markers in plant species have been carried out assuming that comigrating DNA bands are identical or at least have homologous sequences. To test this assumption in garlic, sequence identities of seven polymorphic AFLP markers from two selective amplification primer combinations previously used for similarity estimation in an earlier genetic diversity study were characterized. Among 37 diverse garlic clones, 87 bands from these seven polymorphisms were excised and 2 to 6 colonies were sequenced from each band to yield a total of 191 DNA inserts that were sequence characterized. All sequences contained expected nucleotide sequences of selective amplification primers indicating no error was introduced by AFLP amplification of amplicons due to the mismatches of nucleotides. Among 191 sequences, 124 independent AFLP amplicons were identified since 67 sequences had identical sequences with in a band. Of these 87 bands, 83 bands (95.4%) contained AFLP amplicons that were identical or highly homologous to the typical marker of that band while 4 bands contained one or more amplicons with little homology. Of these 83 bands, 64 (%73.6) contained only highly homologous (>90% sequence identity) and 19 (21.8%) contained both homologous and non-homologous amplicons. We found that 23 out of the 87 bands contained more than one amplicon, and that 37 (29.8%) of the 124 inserts from the 87 bands had non-homologous sequences with sequence identities less than 60%. Sequence conservation of AFLP amplicons followed patterns similar to phylogenetic relationships among garlic clones.