We continue studying 6D,N=(1,1) supersymmetric Yang-Mills (SYM) theory in the N=(1,0) harmonic superspace formulation. Using the superfield background field method we explore the two-loop divergences of the effective action in the gauge multiplet sector. It is explicitly demonstrated that among four two-loop background-field dependent supergraphs contributing to the effective action, only one diverges off shell. It is also shown that the divergences are proportional to the superfield classical equations of motion and hence vanish on shell. Besides, we have analyzed a possible structure of the two-loop divergences on general gauge and hypermultiplet background.