This paper deals with simultaneous scheduling of machines and tools with alternate machines in a multi machine flexible manufacturing system (FMS) to minimize makespan (MS). Only one copy of each type of tools is made available due to economic restrictions and the tools are stored in a central tool magazine (CTM) that shares with and serves for several machines. The problem is to select machines from alternate machines for job-operations, allocation of tools to job-operations and job-operations’ sequencing on machines for MS minimization. This paper presents a nonlinear mixed integer programming (MIP) formulation to model the combined scheduling of machines and tools with alternate machines and a symbiotic organisms search algorithm (SOSA) built on the symbiotic interaction strategies that organisms employ to continue to exist in the ecosystem for solving the scheduling of machines and tools with alternate machines. The results have been tabulated, analyzed. It is observed that there is a reduction in MS when the alternate machines are considered for job-operation.