A particle swarm algorithm is proposed to generate optimal assembly sequences for compliant assemblies. Firstly, the liaison graph and the adjacency matrix describe the geometry of the compliant assemblies. An assembly sequence is represented by a character string, whose length is the number of all parts. The conceptual tolerance analysis is used to evaluate feasible sequences. Thereafter, the particle swarm algorithm is presented to generate assembly sequences, in which the elite ratio is applied to improve optimization results. Finally a fender assembly is used to illustrate the algorithm of assembly sequence generation and optimization.