This research was conducted at Grdarsha Field, College of Agricultural Engineering Sciences, Salahaddin University, Erbil with a GPS reading of (Latitude: 36° 4’ N and Longitude: 44° 2’ E- elevation 415 Meters above sea level). The factorial experiment based on a randomized complete block design using three replicates was done to study the influence of three levels (0, 200, and 400 mg L-1) of each of Zinc and Manganese as foliar application and their combination on their concentration, uptake and fatty acids profile in flaxseed. The results indicate that the Zinc application effect on Zn and Mn concentration with values (0.0032 and 0.0068) % in the treatment (Zn200 and Mn200) additionally caused an increase in the uptake for the two micronutrients in Zn400 and Mn200 with values (15.74 and 14.90) mg plant-1. The treatment combination Zn200 Mn400 caused an increase in palmitic, oleic, linoleic and linolenic acid while the treatment combination of Zn400 Mn200 gained the lowest value. Cluster analysis or dendrogram classified the combination of the two micronutrients Zn and Mn into four main clusters depending on Zn, Mn and the fatty acids profile. The Principal Component Analysis (PCA) shows the angle value between each of the fatty acids and between the two micronutrients is ≤ 90 º which means there was a significant correlation between them and vice versa. There is a very high correlation between linoleic acid & linolenic and F6 while F7 correlated with oleic, stearic and palmitic acid for the vectors for studied traits.