Biodegradable polyhydroxybutyrate (PHB) can be produced from methane by some type II methanotroph such as the genusMethylocystis. This study presents the comparative genomic analysis of a newly isolated methanotroph,Methylocystissp. MJC1 as a biodegradable PHB-producing platform strain.Methylocystissp. MJC1 accumulates up to 44.5% of PHB based on dry cell weight under nitrogen-limiting conditions. To facilitate its development as a PHB-producing platform strain, the complete genome sequence ofMethylocystissp. MJC1 was assembled, functionally annotated, and compared with genomes of otherMethylocystisspecies. Phylogenetic analysis has shown thatMethylocystis parvusto be the closest species toMethylocystissp. MJC1. Genome functional annotation revealed thatMethylocystissp. MJC1 contains all major type II methanotroph biochemical pathways such as the serine cycle, EMC pathway, and Krebs cycle. Interestingly,Methylocystissp. MJC1 has both particulate and soluble methane monooxygenases, which are not commonly found amongMethylocystisspecies. In addition, this species also possesses most of the RuMP pathway reactions, a characteristic of type I methanotrophs, and all PHB biosynthetic genes. These comparative analysis would open the possibility of future practical applications such as the development of organism-specific genome-scale models and application of metabolic engineering strategies toMethylocystissp. MJC1.