The base of nut production in almond is flower buds set with best quality and quantity. Although the process of flower buds set is controlled by genetic characteristics, however it affected with inside and outside diverse factors. To understand relationship between these factors for achieve to annual and regular nut production economically. An experiment was conducted in order to evaluate effects of effective microorganisms (EM) under water stress conditions on bud flower formation in two genotypes of almond trees in Department of Horticultural Science, Faculty of Agriculture, Ferdowsi University of Mashhad, in 2011. In this research effects of two different concentrations (0 and 5%) of EM and three levels of aridity stress treatments (100, 66, and 33% of FC) on number of flower buds in two genotypes (H1and H2) of almond was evaluated. This experiment was arranged as a factorial experiments based on a randomized complete blocks design with four replications. Results showed that the EM increased amount of leaf area, chlorophyll, storage protein, N, K and P in leaves. In this research, effects of different genotypes, EM and irrigation levels on number of flower bud set were significantly different at the %1 level. Number of flower bud formation increased by treatments of EM application, H1 genotype and irrigation level of FC% 100. There was significant interaction between treatments for this trait at %1 level. The best result was obtained from interaction between H2 genotype and irrigation using level of FC% 100 and EM application.