In this paper the two stage assembly flow shop problem (TSAFSP) with bi-objective of number of tardy and makespan minimization is addressed. The problem is known to be NP-hard and is thus solved with two metaheuristics: Simulated Annealing (SA) and Variable Neighborhood Search (VNS) and the Pareto-optimal solutions approach is taken to find optimal solutions of the problem. Computational experiments have been executed and a comparison of the metaheuristics has been carried out. It is indicated that for this problem SA works better in small problems, but is outperformed by VNS as the size of the problem grows; while in general SA is faster than VNS.