Instabilities in the form of periodic or irregular waves at the fluid interface have been demonstrated in microchannel electrokinetic flows with conductivity gradients when the applied electric field is above a threshold value. Most prior studies on electrokinetic instabilities (EKI) are restricted to Newtonian fluids though many of the chemical and biological samples in microfluidic applications exhibit non-Newtonian characteristics. We present in this work an experimental study of the effects of fluid shear thinning on the development of EKI waves through the addition of a small amount of xanthan gum (XG) polymer to both the high- and low-concentration Newtonian buffer solutions. The threshold electric field for the onset of EKI in the XG solution is significantly lower than in the Newtonian solution. However, the propagation speed, amplitude and frequency of EKI waves in the former are all smaller. Increasing the polymer concentration reduces the threshold electric field and as well the critical electric Rayleigh number that considers the fluid property variations in XG solutions. This decreasing trend indicates the enhancing effect of fluid shear thinning on EKI, which is qualitatively consistent with a recent numerical prediction. However, the measured wave properties all follow a non-monotonic trend with XG concentration, different from the continuously decreasing electroosmotic velocity.