The Second Annual Greater Boston Area Quantum Matter Meeting took place in Metcalf Science Center, Physics Department, Boston University, on Saturday, May 9, 2009. The topics of presentation were mainly on quantum systems: strongly correlated systems, atomic and optical systems, and mesoscopics. There were four invited talks, each of about 30 minutes duration and more than thirty contributed talks, each of 4-5 minutes. The schedule is available here. This program was a continuation of the First Annual Greater Boston Area Quantum Matter Meeting, which took place in Jefferson Building, Physics department, on Saturday, May 10, 2008. The link of this meeting can be found in here.