In the last century climate change is a major threat to biodiversity, ecosystem services, and human well‐being. Atmospheric oscillations that occur at the regional oceanic flow pattern may affect significantly the climate of the Earth. In this study, we investigate effects of ENSO (El Nino Southern Oscillation) and NAO (North Atlantic Oscillation) on the Mediterranean crop yield using the Nino 3, Nino3.4, Nino 4, ONI and NAO indices. Olive, which is a bioindicator type in the Mediterranean, and cotton and grapes with high yield and economic value crops were examined. As a method, firstly, Mann Kendall rank correlation test was applied to the yield values of the crops. After the 2000s, it has been determined that the trend of yield has changed and was obtained an increasing trend. Secondly, the correlation between the yields and the indices were determined with the Spearman correlation coefficient. Accordingly, a high correlation of 50% and 80% was found at the p ≤ 0.05 and p ≤ 0.00 significance level in the phenological periods of the crops. The highest correlations were determined especially during flowering period with El Nino indices. The frequency of the correlation detected with the NAO indece is weak. The effect on the efficiency of the phases when El Nino indices are strong was examined graphically. Accordingly, in the 1997 and 2015-2016 periods, when the El Nino phenomen was very stong, there were sharply decreases in the crop yields. It is seriously affects the countries whose economic activity is based on agriculture in the Mediterranean Basin, and it is likely to affect food industry in the future.