This study compares optimization algorithms for efficient estimations of ship's hydrodynamic coefficients. Two constrained algorithms, the interior point and the sequential quadratic programming, are compared for the estimation. Mathematical optimization is designed to get optimal hydrodynamic coefficients for modelling a ship, and benchmark data are collected from sea trials of a training ship. A calibration for environmental influence and a sensitivity analysis for efficiency are carried out prior to implementing the optimization. The optimization is composed of three steps considering correlation between coefficients and manoeuvre characteristics. Manoeuvre characteristics of simulation results for both sets of optimized coefficients are close to each other, and they are also fit to the benchmark data. However, this similarity interferes with the comparison, and it is supposed that optimization conditions, such as designed variables and constraints, are not sufficient to compare them strictly. An enhanced optimization with additional sea trial measurement data should be carried out in future studies.