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Wood rot of floor joists is typically not covered by a homeowner policy unless it can be tied directly to a covered event.

Typical home insurance policies provide coverage for damage that is “sudden and accidental.” For example, the accidental discharge or overflow of water from a household appliance is a peril covered by most homeowner policies. 

Thus, if a pipe burst and caused water damage to your floor joist, then at the time of the damage you likely could have made a claim.  Instead, it appears that the rot isn’t caused by a certain event but as a result of aging materials and perhaps poor maintenance.

For the mold to be covered, it also would have to be associated with a covered peril, like a burst pipe.  Mold caused by water due to condensation, excessive humidity or flooding is typically excluded from coverage provided by a home insurance policy.  (See “Mold coverage hard to find in home insurance policies.”)