Methane (CH4) is the major chemical component of natural gas, as well as a particularly potent greenhouse gas. Methanogens are the archaeal organisms that produce methane and play a key role in biological methanogenesis. A total of six taxonomic orders of archaeal methanogens have been discovered and almost all previous phylogenetics studies have confirmed that these methanogens are genetically diversified and do not belong to a phylogenetically monophyletic group. To date, the relationships between methanogens and closely related non-methanogen species at the taxonomic order level remain unresolved and different studies have often produced contradictory results based on different gene markers. These studies suggest the complicated and distinct evolutionary histories between different genes in these genomes. In this thesis, 74 fully sequenced archaeal genomes, including 41 methanogens, were collected and used in a comprehensive comparative genomics and evolutionary analysis. First, numerous phylogenomic trees were reconstructed based on various datasets using several methods and the results show that Methanopyrales is close to Methanobacteriales (or Methanopyrales) in the statistically best species tree. In addition, Methnocellales and Methanosarcinales, and as well as Methanomicrobiales and Halobacteriales are sister clades in the best species tree, but the confidence level is low. Further incongruence tests among the phylogenetic forest, which is composed of 3,694 ortholog gene families, reveal that the archaeal core genes have much stronger consistent vertical evolutionary signals than other genes, but these core genes are not topologically fully congruent with each other. Secondly, a series of weighted network analyses were implemented to decompose the hierarchical structure and to reveal the co-evolved gene modules, global and local features in the archaeal methanogen phylogenetic forest. The results show that this co-evolution network contains 7 statistical robust modules, and the module with the highest average node strength includes the majority of the core genes located in the central position of the network. Further in-depth evolutionary analysis reveals that the modularized evolution in the archaeal phylogenetic forest is closely related to the time of origin, HGT rate and ubiquitous vertical inheritance in gene families. Lastly, to investigate the causes for and factors related to the pervasive topology incongruence in the phylogenetic forest, in-depth clanistics analysis and HGT detection were carried out. These results show that (1) about 63% of gene families experienced at least 1 HGT event in their whole history; (2) core genes are not immune to HGT but they do have much lower HGT rates than other genes; (3) methanogens have distinct trends of HGTs from non-methanogen species; and (4) highly frequent inter-order HGTs, even for core genes, in methanogen genomes lead to their scrambled phylogenetic relationships. Further clanistics analysis screened out 119 candidate genes related to methanogenic pathways adaptation and most of these gene families have experienced at least one HGT. In conclusion, a complex evolutionary scenario for methanogenic archaeal species was described in this thesis as a combination of complicated vertical and non-vertical evolutionary processes in a modularized phylogenetic forest. / published_or_final_version / Biological Sciences / Doctoral / Doctor of Philosophy