If one atom is identical to another, we can say they are the same chemical species.
If one molecule is identical to another, we can say they are the same chemical species.
Examples
A balloon full of pure helium contains atoms of the same chemical species.
A balloon full of oxygen, O2, is filled with molecules of the same chemical species.
A bottle full of pure water, H2O, is filled with molecules of the same chemical species.
A pure gold ingot contains atoms of the same chemical species.
Tightening up the Definition
We can make the definition more precise by saying that to be of the same species, the atoms or molecules must share the same set of molecular energy levels on the time scale of the observation.
For example, a mixture of two conformational isomers may be interconverted sufficiently slowly to be detectable by different NMR spectra and hence would be separate chemical species on the timescale of the spectrometer's frequency.
On the other hand, in a slow chemical reaction the same mixture of conformational isomers may behave as a single chemical species, i.e. there is virtually complete equilibrium in the molecular energy levels belonging to the two conformers.
Except where the context requires otherwise, a group of molecules containing different isotopes in their natural abundances will be regarded as all being the same species. Groups of atoms are treated in the same way.
The definition of "species" encompasses cases such as graphite, sodium chloride, or a surface oxide, where the basic structural units may not be capable of isolated existence, as well as those cases where they are.