Fumaria species belong Fumariaceae family are rich in isoquinolines, protoberberine and quaternary protoberberine alkaloids used in traditional medicine. Fumaria vaillantii were collected from central zone of Saveh. In this research was describes determination and identification of tertiary bases in alkaloid extracts the F. vaillantii by quaternary extract method, spectrophotometry, TLC and GC-MS techniques. Fruits and leaves of F. vaillantii and F. asepala had the highest alkaloids content. Total alkaloid of fraction 2 (quaternary benzophenantridine alkaloids, protopine alkaloids) was higher than other alkaloid fractins. There were 10 and 8 types of alkaloids in all fractions of F. vaillantii and F. asepala in the TLC analysis, respectively. The some new compounds include 6-amino-5-pentenoic-alpha-Lactame, 1H-imidazole and 1,10-dicyanodecane in fraction 1 of F. vaillantii and 4-(2'-hydroxy-3'-iso propyl amino propoxy) phenylacetic acid and 6-amino-5-pentenoic-alpha-Lactame in fraction 4 of F. asepala were determined by GC-MS analysis. F. vaillantii and F.asepala had some quaternary protoberberine alkaloids but they were different from other reported compounds. A number of compounds of α-Lactams (Aziridinones) presented in alkaloids of F. vaillantii and F.asepala. Traditional antibiotics antibiotics penicillins, penems and cephalosporins are Beta-Lactam compounds. Antifungal activity was evaluated using the culture of round disks of Aspergillus on the medium contain different concentrations of the alkaloid fractions. The all alkaloid fractions in varies concentrations exhibited broad spectrum inhibition against Aspergillus flavus and A. niger. The minimum concentration and the maximum fungicide concentration against the test Aspergilluses were 0.04 mg/ml and 0.12 mg/ml of the all fractions, respectively. Our results showed that F. vailantii have four type alkaloids with high anti Aspergillus effects.