Study and design of active control strategies for transition in boundary layer flows is done within this project. The control strategies are designed using the optimal-control approach to control of the Navier-Stokes equations and use the adjoint-equation technique for associated gradient computations. Linear optimal control techniques based on the Riccati equation are also explored, where spatially localized convolution kernels have been obtained for both control and estimation. The strategies are applied to control or delay of bypass transition as well as other flow instabilities. The performance of these control laws is quantified in direct numerical simulations by computing transition thresholds. We have shown that the threshold values can be increased by about 500% for random perturbations. By using a physically motivated modification of the objective function we have shown that the linear controllers are also able to relaminarize a low Reynolds number turbulent flow. A new direction of this research is to calculate and evaluate these controllers and estimators for more complicated boundary layer flows such as Falkner-Skan and Falkner-Skan-Cooke flows.