This paper focuses on the development and implementation of a Genetically Tuned Fuzzy Scheduler (GTFS) for heterogeneous FMS under uncertainty. The scheduling system takes input from a table and creates an optimum master schedule. The GTFS uses fuzzy rulebase and inferencing where fuzzy sets are generated by a genetic algorithm to tune the optimization. The fuzzy optimization is based on time criticality in deadline and machine need, taking into account machine availability, uniformity, process time and selectability.