Both PCR and molecular cloning can be used to direct the replication of DNA sequences. There are several fundamental differences between these two methods.
Molecular cloning replicates DNA within in a living cell, while PCR replicates DNA in an in vitro solution, free of living cells.
Molecular cloning involves cutting and pasting the sequences, while PCR amplifies DNA by copying an existing sequence.
DNA cloned by molecular cloning is usually faithfully copied and fully functional, whereas PCR introduces errors in sequence, resulting in mutations.