Mucilage is one of the key components of flaxseed (which is also called linseed), and exhibits unique functional properties such as high water-holding capacity, and foamability. As a result, flaxseed mucilage has applications in food, agriculture, medicine and other industries. The composition and functional properties of mucilage vary between genotypes. To explore this variation, we characterized the mucilage of nine diverse varieties of flaxseed according a range of parameters including: morphology, mucilage content, fibre content, minerals, phenolic acids, polyphenols, antimicrobial activity, and antioxidant activity. We found significant differences between the genotypes in almost all of the parameters tested. Furthermore, we found a strong correlation between several of these parameters, including antioxidant activity, hydroxycinnamic acid, and sugar content. Antimicrobial activity against Gram positive bacteria was correlated with fibre content and potassium content, while chlorogenic acid content was correlated with suppression of Gram negative bacteria. These results provide a framework for crop improvement further development of functional and value-added products from flaxseed.