A completely separated functional FMS (Flexible Manufacturing Systems), or a partly separated functional FMS, should be constructed because a fully functional FMS, where each machine has all of the tools required for procesing various kinds of jobs, is superflous and wasteful in meeting the multiform and changeable demands of comsumers in a flexible manner. The effective methods are presented in this study for allocating the tools to each machine in a two-machine flow shop type FMS to meet the above demands and to maximize the utilization of the FMS. The methods for a completely separated functional FMS having no duplicated tools and a partly separated functional FMS having some duplicated tools are proposed in this paper. Some simulation results clarify that utilization of the FMS by this methods is as high as the fully functional FMS when the number of jobs is large.