Atoms and molecules both make up matter in the universe, but atoms make up molecules. In order to form molecules, atoms form bonds.
These bonds can number in the hundreds of thousands, as in the unusual (and man-made) case of PG5, which has 170,000, or they may be singular, as in the case of a hydrogen molecule (H2). A water molecule is formed of two hydrogen atoms and one oxygen atom, hence its molecular name of H2O.
In discussing atoms and molecules, a third commonly used term is 'element.' Elements are the kinds of atoms that exist, including hydrogen or oxygen, as displayed in the periodic table.