Plant taxonomy is considered an important branch of science; it needs highly professional taxonomists to classify plants depending on their morphological characteristics but this method has numerous disadvantages, it is time-consuming and highly dependent on plant growth stages and reproductive organs (such as tree species with a short bloom period or rarely blooming). Therefore, several molecular techniques (DNA fingerprinting, DNA barcoding, Next generation sequencing) have been used to overcome these obstacles. DNA barcoding is considered the bedrock to classify and discover different plant specimens by combining the strengths of molecular genetics, sequencing technologies and bioinformatics by using highly variable short regions of DNA. Four gene regions (rbcL, matK, trnH-psbA and ITS) have been utilized as the universal DNA barcodes for plants. The combination of two or more barcode regions improves the resolution level and provides perfect huge data for species identification. DNA barcoding faces many obstacles for discrimination of some plant specimens for example the presence of conserved ancestral alleles, high intraspecific variability and some other factors, As an outcome, it was proposed to use complete chloroplast sequences using next-generation sequencing (NGS) technique. NGS technique is highly expensive thus it was needful to use other new and cheap techniques such as genome skimming and twin track processes.