Provided are a rubber composition achieving balanced improvement in processability, fuel economy, rubber strength, abrasion resistance, and wet-grip performance, and a pneumatic tire thereof. The rubber composition includes a conjugated diene polymer and a silica having N2SA of 40-400 m2/g, the polymer being obtained by polymerizing a monomer component including a conjugated diene compound and a silicon-containing vinyl compound in the presence of a polymerization initiator of formula (I): to produce a copolymer, and reacting a compound containing nitrogen and/or silicon atoms with an active terminal of the copolymer, wherein the amount of the diene polymer is 1-60% by mass and the amount of polyisoprene-based rubber is 0-99% by mass, each per 100% by mass of the rubber component; the amount of the silica is 10-80 parts by mass per 100 parts by mass of the rubber component; and the composition has a carbon ratio of at least 50.