An exciting new division of soil science is emerging in line with the development of biotechnology and environmental microbiology. We may name it Soil Macromolecular Chemistry. The emergence of this subject is in line with the development of modern molecular microbial ecology and the multidisciplinary interaction. We suggested a concept of the chemistry of soil macromolecules. Clay minerals, clay oxides, humic substances, proteins (enzymes) and DNA are soil inorganic and organic macromolecules. The composition, structure, characteristics and reactions are the main research contents of the soil macromolecular chemistry, and the interaction mechanisms among these macromolecules are the core of the subject. The theory and the developed technology are important bases of molecular microbial ecology. The emphasis of current soil microbial ecology has shifted from conventional culture to molecular microbial ecology based on modern molecular biotechnology. Molecular ecology has entered the stage of the genomics or even post-genomics, i.e., proteomics. More than 100 microbial genomes have been established and soil microbial metagenome or ecogenome are becoming hot points of soil microbial ecology, and soil proteomics is in its infant stage. The bottle-neck limiting the soil microbial genomics and proteomics is how to obtain representative, large size DNA and proteins, and how to separate extracellular and intracellular protein and gene expression products. Thus understanding the interaction mechanisms among soil macromolecules, developing separation technology of DNA and protein from soil matrix, are important pre-requisite for molecular microbial ecology. Soil microbial biological approaches have received more and more application in environmental bioremediation, biological resource utilization, developing new medicine or have great potential. We predict that the hotspot of molecular biology will shift to environmental genomics and proteomics after human genome plan, rice genome plan, microorganism genomes and functional genomics etc. On that time, a new term may appear as soil macromoleculomics which studies soil macromolecules—DNA and proteins.