MapReduce uses InputFormat and RecordReader classes to read input data from various sources and formats. InputFormat determines how input is partitioned for map tasks, while RecordReader reads the data and returns key-value pairs. Similarly, OutputFormat and RecordWriter are used to write reducer outputs - OutputFormat validates the output sink and RecordWriter writes each output as a key-value pair. Implementing these classes allows MapReduce to support different data formats and storage mechanisms in a flexible way.