This book collects the refereed proceedingsof the Second International Conference on Algorithms and Discrete AppliedMathematics, CALDAM 2016, held in Thiruvananthapuram, India, in February 2016.The volume contains 30 full revised papers from 90 submissions along with 1invited talk presented at the conference. The conference focuses on topicsrelated to efficient algorithms and data structures, their analysis (boththeoretical and experimental) and the mathematical problems arising thereof,and new applications of discrete mathematics, advances in existing applicationsand development of new tools for discrete mathematics.