Use of greenhouse cultures accompanied by new techniques such as soilless or hydroponic culture on the one hand improves suitable control of plants nutrition and on the other hand it has created a great progress in greenhouse productions. In order to greenhouse tomato cultivar of Hamra was cultured in a hydroponic system and effect of micronutrients different levels was studied on it. The experiment design was as randomized complete block with five treatments and four replications. Experimental treatments were included: Lack of micronutrients application, Full application of sulfate manganese (4.06 mg/lit), Full application of sulfate zinc (4.42 mg/lit), 50% sulfate manganese (2.03 mg/lit) + 50% sulfate zinc (2.21 mg/lit) and Full application of sulfate manganese + Full application of sulfate zinc. The results showed that the highest fresh fruit yield, fruit dry matter percentage and content of Mn and Zn in fruit obtained from full application Mn, Zn and Mn + Zn. However micronutrients different levels had significantly effect on content of nitrogen, but they haven’t significantly effect on fruit size of tomato.