This study was carried out to investigate the effects of 7-day-old fungal filtrates of Aspergillus niger and Penicillium chrysogenum isolated from maize seeds on percentage germination, morphological and anatomical structures of maize seedlings. The seeds were soaked in culture filtrate of each fungus for 12hrs before planting. Blotter method was used to observe seed germination. Results showed that the percentage germination of the seeds treated with culture filtrates of A. niger and P. chrysogenum (65.33% and 79.67% respectively) was lower than the control (100%) and significantly different from each other at significant level of P≥ 0.05. The leaf area showed significant difference between the experimental and control plants but there was no significant difference in the leaf number. The tetracytic stomatal complex type and wavy anticlinal walls remained constant in all the treatments and control. The stomatal index of seed treated with A. niger on abaxial leaf surface (43.61%) showed significant difference with adaxial leaf surface (31.97%). The treatments had no significant difference on stomatal density at abaxial surfaces. Reduction in stomatal size and density suggests physiological implication.© JASEM