Polygonum and Scrophulariaceae Herbs such as roots and tubers produced in Guizhou were studied, to analysis the concentrations of heavy metals in roots, stems and leaves, and to compare the heavy metal content in roots and stems of Polygonum collected from different production places in Guizhou. The results showed that the contents of 5 kinds of heavy mentals, such as Cu, Cr, Cd, As and Pb, in roots of Polygonum were lower than that in stems and leaves. For the roots of Scrophulariaceae, of which heavy metal content except Cu was far below that in stems and leaves. The content of Cd in the whole Scrophulariaceae and Pb in leaves were beyond the limit of the indicator of the Green Industry Standards of Medicinal Plants and Preparation of Foreign Trade (WM/T2-2004). The enrichment of Cr and Cd in different parts of Polygonum,Scrophulariaceae was the same, for Cr, leaves>stems>roots; and for Cd, stems>leaves>roots, the content of Cd in roots of Scrophulariaceae was much larger than that of Polygonum, which could prove that the roots of Scrophulariaceae were easier to enrich Cd than that of Polygonum. The contents of Cu, Cr, Cd, As and Pb in the stems of Shibin Polygonum were higher than that in the roots of Duyun Polygonum, the contents of As, Pb in roots of Shibin were lower than that of Duyun Polygonum, the remaining heavy metal contents were higher than that of Duyun Polygonum.