To reduce the negative impact of chemical fertilizers and increase soil fertility, organic fertilizers must be used which have a great potential to improve the biological, chemical, and physical properties of the soil. This study had been conducted to study the effect of different local manures ( alfalfa, chicken, and sheep) on soil enzymes activity (Asparaginase enzymes and Alkaline Phosphatase), which they essential enzymes responsible in releasing nutrients needed by plants, at different conditions of incubation temperatures(28C and 35C) and duration (two and four weeks), results indicated that the highest Asparaginase enzymes activity (143.85ppm) was recorded in soils added by chicken manure after incubating it for 4 weeks at 28C, while the lowest activity showed at 35C incubated at the same period. the highest rate of Alkaline Phosphatase enzyme (150.92 ppm) was found after two weeks of incubation at 35C in soils treated with alfalfa manure while at 28C incubation temperature resulted in lowering of enzyme activity. Molecular analysis of soil showed difference among treated soils with different manures in quality of soil microorganisms. From results noticed that source of organic matter, incubation period and temperature have great effects on enzyme activity and type of soil microorganisms.