Abstract: One of the challenges of contemporary bioinformatics is how to make use of the large volume of data and information from genome sequencing and high-throughput genomic studies for the analysis of large-scale metabolic networks. This article first briefly reviews the reconstruction of metabolic networks from genome information and the graphic methods for the analysis of these genome-based networks. This is followed by a survey of the two most promising concepts for the analysis of network-based metabolic pathways, namely the elementary flux modes (EFMs) and the extreme pathways (EPs) and their applications that include the analysis of structure properties and functions of metabolic networks and the design and analysis of engineering strains.The challenges and possible solutions to combining the genomic information and the above mentioned pathway analysis methods for a genome-wide understanding of metabolic pathways and their regulation are discussed.