Molecular methods have become non-replaceable for the improvement of food production and its control. The Department for Biochemistry and Genetic Engineering (DBGE) as a part of the Faculty of Agriculture Sciences and Food is a crucial entity using molecular techniques in different areas of agriculture and livestock production. DBGE is mainly dealing with marker assisted selection (MAS), evolutionary studies; determine the origin of food products; enzyme analysis in food processing; transcriptional and translational analyses; molecular detection of plant viruses; and GMO analysis. The target molecules were proteins, RNA and DNA. MAS is systematically applied in animal breeding in Macedonia using RYR-1,  and S1-casein genes. Evolutionary studies were performed using DNA microsatellites to estimate genetic distance among autochthonic strains of sheep and tomato varieties. The identification of food products origin and gender identification in fish were done using protein profiling. Gene expression was studied analysing different growth factors and inhibitors at RNA level. More than 3.000 plant and animal samples were analysed in the Laboratory for biochemistry and molecular biology. GMO laboratory as a part of the DBGE is the first authorized facility for GMO testing of food and feed samples. In more than 100 samples RT PCR methods were used.