Mycotoxins are low molecular weight secondary metabolites that can increase the fungal pathogenicity. This research was carried out with the aim of investigating the effect of Alternaria toxins on tomato and geranium plants in Birjand during 2016-2018. Alternaria isolates were recovered from Birjand soil using Czapak Agar media and identified based on the morphological and molecular characteristics. Mycotoxin production was carried out by culturing Alternaria isolates in the PDB medium for 21 days at 25 to 27 °C. Toxin extraction was performed by removing the fungal mycelia from PDB media culture by centrifugation after adding the chloroform-acetone (88/12) solution. A two-phase solution was created after centrifuge that chloroform-acetone phase was isolated, air dried and dissolved in methanol. Mycotoxins were identified by high-performance liquid chromatography (HPLC) technique. One millilitre of distilled water was added to air-dried toxins and injected into the geranium and tomato leaves with a syringe. Leaves tissue reaction was studied ten days after toxin injection. Based on the morphological and molecular characteristics, the toxigenic isolates of this study belonged to Alternaria sp. Alternariol (AOH), altenune (ALT), alternariol monomethyl ether (AME), tentoxin (TTX) and tenuazonic acid (TeA) toxins were identified in the Alternaria isolate of this research. Toxins induced chlorosis and necrosis in the tomato leaf tissue four days after injection. The injection of these metabolites did not affect the geranium leaf tissue after ten days. This research is the first report of the identification of these five toxins in Alternaria isolates and their effects on Geranium and Tomato tissues in the Birjand region.