As products of interaction of time and space, geoherbs, which are essential parts of Chinese Materia Medica, were characterized in different morphology, unique habitat, continuous and changeable sites. The main fields in molecular mechanism of geoherbs focus on: biodiversity and molecular identification, genetic different and evolutionary genetics, geo-variation and environmental adaptation, germplasm and aimed genus choosing, expression and control of functional gene, gene transfer and bio-safety evaluation. The main tasks are to discover the genetic variation at molecular level, ascertain the molecular characteristics of geoherbs and the effect of environment on gene expression of geoherbs, confirm the genetic factors attribute to the forming of geoherbs, and find out the genetic basis of geoherbs at individual level and population level, respectively. This paper pointed out that the essential of geoherbs is continuers quantities variation at population level, geoherb's populations are different in gene frequency with the others'; geohersm are quantitative trait loci (QTL) controlled by multi - gene or combination with multiple-gene and major gene at individual level. It is very important to pay more attention to the scale effect of geoherbs, refer the theories and methods of quantities genetic, and concern more about the interaction of environment and gene in geoherbs' molecular mechanism research.