Synthetic fungicides are used in the cereals production to reduce the fungal incidence and consequent production of mycotoxins, however due to toxic effect of these compounds, alternatives are natural sources that perform this protection function. Microalgae of the genus Nannochloropsis and Spirulina contain compounds with antifungal actions already demonstrated, in this study it was tried to evidence the effect of phenolic extracts of the microalgae in the inhibition of the activity of the enzyme α-amylase. The phenolic extracts and tebuconazole (fungicide commercially used in the control of fungal infections in wheat) were applied to petri dishes containing agar in the presence and absence of wheat grains. The Fusarium isolate was inoculated at the center of each plate, and were incubated at 25°C with light-dark 12 h photo-period. After 24 h and 168 h of incubation, the α-amylase activity was determined by the estimated starch degradation by iodometric method. When the extracts were applied to the agar, the enzyme inhibition occurred in 24 h, increasing at the end of the incubation period at levels of 82, 69 and 78% for the extracts of Nannochloropsis sp., Spirulina sp. and tebuconazole, respectively. When applied to wheat grains only the phenolic extract of Nannochloropsis sp. maintained inhibition of the enzyme above 60% throughout the assessed period. The extract of Spirulina sp. inhibited the enzyme only in the initial period of biomass development and tebuconazole resulted in small inhibition at the end of the period (17%). In the case of incubation of grains together with the strain of F. graminearum the development of the fungus itself may be promoted by enzymes from the germination seed process or by Fusarium production. In this case, phenolic compounds from Nannochloropsis were able to avoid the Fusarium development due to inhibit enzymes endogenous and exogenous present the culture media.