Trigonella foenum-graecum L. is a widely used herb in traditional medicine. The aim of this study was to evaluate the genetic polymorphisms in fenugreek plants following the treatment of fenugreek seeds with different combinations of biotic and abiotic agents using the random amplified polymorphic DNA (RAPD)-PCR technique. We assessed the effects of two strains of the fungus Trichoderma harzianum (Th-1 and Th-2), methyl jasmonate (MeJA), and Aloe vera gel (AVG) on growth parameters of fenugreek plants. Combinations of Th-1, MeJA, AVG significantly increased fenugreek root length, shoot length, shoot fresh weight, number of true leaves, and chlorophyll content. The Th-2 isolate, on the other hand, markedly slowed plant development (except for root length which was not affected significantly). In contrast, the combination with MeJA had no considerable effect on all growth measures, whereas the combination with VAG resulted in a substantial drop in shoot height and chlorophyll content when compared to other growth parameters that were unaffected. The present study has shown that the PCR amplification of DNA, using five primers for RAPD analysis, produced 62 DNA fragments that could be scored in all genotypes. The total number of polymorphic bands was 26, and the average percentage of polymorphism was 54.21%. The RAPD-PCR results showed that the treatment of fenugreek seeds with Th-1 alone or in combination with MeJA and AVG induced polymorphisms in fenugreek leaves.