This research was performed in a completely randomized block design with four replications to investigate zinc (Zn) and manganese (Mn) nutrition effects on greenhouse tomato (Lycopersicon esculentum Mill. cv. HAMRA) in a perlite-containing media. Experimental treatments were: (1) control (Mn and Zn-free nutrient solution), (2) application of Mn in a concentration equal to the full Hoagland’s nutrient solution (4.06 mg/l), (3) application of Zn in a concentration equal to the full Hoagland’s nutrient solution (4.42 mg/l), (4) application of Mn and Zn in concentrations equal to the 50% Hoagland’s nutrient solution (2.03 mg/l Mn + 2.21 mg/l Zn), and (5) application of Mn and Zn in concentrations equal to the full Hoagland’s nutrient solution (4.06 mg/l Mn + 4.42 mg/l Zn). Results showed that the highest fresh-fruit yield, fruit and leaf dry matter and content of Mn and Zn in fruit were obtained from single or combined application of Mn and Zn in concentrations equal to the full Hoagland’s nutrient solution. In addition, Zn and Mn nutrition significantly affected the fruit concentrations of crude protein, nitrogen and phosphorus, while the effect of these treatments on fruit size of tomato was not significant.