The use of mahagoni timber began long time ago from the eighteen century in the Caribean islands. It was first used as a substitute for the oak timber for shipbuilding. However, this tree is now endangered. This study highlighted the new super mahagoni tree that is tolerant unfavorable environment and which is the only survived one from one hundred trees that were cultivated in Nobaria location. This study was designed to screen morphological attributes and describe similarity and diversity in terms of isozyme, RAPD and ISSR profiles of three genotypes of Swietenia mahagoni and to compare them and investigate a new genetic resource (Nobaria location). Three different genotypes of Swietenia mahagoni were obtained from Alexandria governorate, timber tree department orchard of Horticultural Institute Research, Giza governorate and North Tahreer region, Beheira province. Soil characterization was done. Antioxidant compounds were extracted and determined for the samples. Isoenzyme electrophoresis was done. Characterization of three different genotypes of Swietenia mahagoni at molecular level was done. Also, sequence repeat was done. Results revealed that calcium carbonate contents of the samples were found to be high which causes the fixation of the phosphorous. Total phenolic compounds, flavonoid content and antioxidant activity were found to be of a significant difference among the three genotypes. The highest flavonoids content was observed in the leaves of Alexandria tree genotype. Our results indicated that trees grown in salinity (Nobaria tree genotype) conditions had the highest amount of total phenolics, total flavonoids and total antioxidant compared to trees grown in non-saline conditions. The results found that Nobaria genotype bands had higher densities and intensities than in the other two locations in peroxidase and polyphenol oxidase banding pattern. At the molecular level, four RAPD-primers displayed a total of 42 DNA fragments were detected, in which 26 (61.90%) were polymorphic fragments. However, 16 bands were common (monomorphic) for the three genotypes. In ISSR analysis, 6 of the ISSR primers generated variable banding patterns. A total of 39 out of 62 ISSR fragments were polymorphic. 28 amplified fragments were considered as cultivar-specific markers. Results of the combination of the banding patterns of both techniques, wood chemistry revealed that high level of variation was on Nobaria mahagoni tree station which recorded high extracts percentage against Giza that recorded the lowest percentage. Hemicelllose analysis showed that the tree of Nobaria recorded the highest percentage compared to corresponding trees in Alex. and Giza. Fiber length analysis showed that Nobaria tree recorded the tallest fiber length against the two other locations. In conclusion, similarities and differences were identified between the three genotypes and proved that pattern resistant genotype of Swietenia mahagoni, cultivated at Nobaria, Horticultural Research Station, Egypt showed good tolerance to unfavorable environmental conditions (salinity and calcareous soil).
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