Memory mapped I/O and isolated I/O are two methods for interfacing I/O devices with the CPU. With isolated I/O, memory and I/O devices have separate address spaces and control lines, allowing special I/O instructions. With memory mapped I/O, memory and I/O share the same address space and instructions, treating I/O as memory, but reducing available memory addresses. Both methods have advantages like flexibility and speed, but also disadvantages regarding complexity and available address space.