The Great East Japan Earthquake disturbed coastal regions facing the Pacific Ocean. Subsequent infrastructure reconstruction in the coastal region of southern Sendai Bay has now become a major threat to biodiversity. The recovering coastal forest zone has been artificially filled and re-planted with pine trees. Seawalls are being reconstructed by strengthening remnant structures. Here, we present five lessons learned through studying the reconstruction process. 1) Monitoring and evaluation of biodiversity before disaster strikes can provide indispensable data for prioritizing actions after ecological devastation. 2) Development of methodologies and policies for rapid environmental assessment are essential. 3) The effects of large, infrequent disasters on biodiversity should be studied. 4) Scientists should prepare procedures for dealing with scientificproblems that arise at the time of disaster and afterwards. 5) Development of policies and technologies for ecosystem-based ('green') infrastructure reconstruction is important for enlightened management of disaster effects on human populations and for biodiversity conservation.