A substance is monatomic if it is made from atoms that form no permanent bonds. While forces may exist between atoms, there is no fixed structure. Examples include the noble gasses which have a stable configuration of electrons without needing to form bonds.
In contrast, a molecular substance is made from atoms joined together by covalent bonds. By forming a bond, atoms in a molecule share electrons and become more stable. This means energy is required to break molecules apart.
A molecule may have different properties to substances with the same constituent atoms. Water (H2O) is not very flammable whereas hydrogen gas (H2) is.