The majority of breeding programs of edible mushrooms are carried out in the white button mushroom due to its commercial importance and genetic difficulties. In this research, for the first in the country, it was possible to examine intra-hybridization and its effect on both productivity and mycelium morphology in a potentially commercializable one. Also, for the first time, potential of molecular AFLP markers to the button mushroom breeding was examined. The strains comprised six heterokaryons and four homokaryons from different sources that 214 single spores were then isolated from heterokaryons. Selected slow and very slow growing isolates were used in fruiting test (performed in an industrial mushroom farm) resulting in preparing 25 homokaryons. Having 29 homokaryons, 406 diallele crosses were performed from which 145 crosses were compatible. Productivity of compatible crosses was examined in an industrial mushroom farm on a randomized complete blocks design basis with two replications. Nine hybrid strains which their yield was significantly higher than the control were used in yield trials performed in two industrial mushroom farms on a completely randomized design basis with three replications. The yield of three hybrids was significantly higher than the control. In these trials, economically quality of fruiting bodies was also studied. The hybrids number 3 and number 8, having a yield higher than the control, had a desirable economically quality. After nine months and three subcultures, mycelial growth stability of the nine hybrids was investigated from which the hybrid number 8 had a considerable stability. For the nine hybrids, a strain registration was provided. This strain registration pointed some interesting notes particularly about study of pedigree of offspring having high performance than the control which will be useful in designing the following breeding programs. Genomic DNA extraction was performed using the compatible hybrid strains and the control. Enzymatic restriction was performed by endonuclease restriction enzymes, EcoRI and Tru9I (an Isoshisomer of MseI). Ligation was then carried out by oligonucleotid double stranded adaptors. Pre-selective PCR was performed by using one pair primers, designed on the basis of adaptors with one selective nucleotide in 3' end, and selective PCR was carried out by the same primer, but with two selective nucleotides in 3' end under a three way program. PCR products were then denaturized by polyacrylamide gel 7%, and stained by silver nitrate. AFLP profiling was successfully prepared for 14 samples out of 145. Monomorph and polymorph markers were numbered and relevant data were put to software PopGene32 for dominant markers. Dendrogram was drawn by using software JMP4. In one of measurements for six samples, 38 scorable alleles were identified that 29% of them were polymorph and 71% of them were monomorph. The results showed that AFLP is a potent technique for genetic fingerprinting of the button mushroom strains, because in this research with one AFLP site (only one pair primer); it was possible to distinguish individuals. Thus it is possible to prepare a molecular strain registration for each individual. The result also showed that the AFLP profiling is replicable and reliable.