I think the official documentation gives you the answer to this one (albeit in a fairly nonspecific way):

This method is the dynamic equivalent of the Java language instanceof operator.

I take that to mean that isInstance() is primarily intended for use in code dealing with type reflection at runtime. In particular, I would say that it exists to handle cases where you might not know in advance the type(s) of class(es) that you want to check for membership of in advance (rare though those cases probably are).

For instance, you can use it to write a method that checks to see if two arbitrarily typed objects are assignment-compatible, like:

publicboolean areObjectsAssignable(Object left,Object right){return left.getClass().isInstance(right);}

In general, I‘d say that using instanceof should be preferred whenever you know the kind of class you want to check against in advance. In those very rare cases where you do not, use isInstance() instead.

if(foo instanceofThisClassIKnowRightNow)...

if(someObject.getClass().isInstance(foo))...