Structural equation modeling (SEM) was applied here to modify the ordinary weights-of-evidence (WofE) method for calculating posterior probability to improve conditional independence (CI) in the application of this method mineral potential prediction. The new method attempts to reduce the effect of CI by defining new binary patterns with an optimum combination of cutoff values of patterns. The solution is calculated through SEM, and the goodness of fit between evidence and mineral deposit occurrences is evaluated by a specified target function. The main difference between the new WofE and ordinary WofE is that evidence in the new method maintains a balance between the significance for mineral potential prediction and CI, rather than the significance for mineral prediction only as in ordinary WofE. A case study of prediction of potential for hydrothermal Au mineral deposits in Nova Scotia, Canada, is discussed here. The results indicate that the new method performs better than the ordinary WofE.