First difference:

instanceof is a reserved word of Java, but isInstance() is a method of java.lang.Class.

Other differences:

you could use instanceof on types (which are known on compile time), and isInstance() could only be called on an instance fo java.lang.Class.

if (obj instanceof MyType) {
...
}


if (MyType.class.isInstance(obj)) {
...
}

so you can have dynamism using isInstane() like this:

   Class x = Integer.class;

   if (x.isInstance(obj)) {
   ...
   }

   x = String.class;

   if (x.isInstance(obj)) {
   ...
   }

as you see you could check the type of an object with an unknown class during compile time!