The molecular marker based identification techniques are extremely reliable methodologies that are currently used in forensic crime investigation of human, animals as well as plants. Generally the markers are short tandem repeats (STRs), species specific primers, SNPs (single nucleotide polymorphism) are based on PCR and NGS methods which is still under extreme investigation by FBI for development of more convenient, easy and reliable procedures. The human DNA profile generated through genetic analyzer (Electrophoresis of amplified STR markers) is the most used method which dealt with murder, sexual assault, rape, paternity dispute and physically burnt cases. However, the interpretation of results become difficult in cases of partial profiles generated from challenging forensic samples such as dead cells or mixed DNA profile and sometimes very difficult or impossible in case of monozygotic twin’s. The advances in NGS platforms applied in generation of DNA database from different sources, phenotypic analysis or phylogenetic analysis and can be used in analysis of mixed DNA identification, complex paternity cases, monozygotic twin’s identification, body fluid analysis, as well as species origin detection in forensic science. Recently, it has been reported protein can be also used in the identification of humans as the variations can be unique to an individual or a community of people. Thus, the advent of unique protein based human identification process might be an asset in forensic investigation which is the major new era challenge in forensic science.