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Chemical species are atoms, molecules, molecular fragments, ions, etc., being subjected to a chemical process or to a measurement. Generally, a chemical species can be defined as an ensemble of chemically identical molecular entities that can explore the same set of molecular energy levels on a defined time scale. Chemists also use chemical species to mean a set of chemically identical atomic or molecular structural units in a solid array.
For example, when molecules of NaCl dissolve in water we don't really have any NaCl as such in the solution. We have Na+ and Cl- ions because NaCl dissociates. We say the species present in solution are Na+(aq) and Cl-(aq). In this case, the species present in solution are the ions. In other cases, where the molecules don't dissolve in water, we would have molecular species in solution rather than ionic species.
In supramolecular chemistry, chemical species are those supramolecular structures whose interactions and associations are brought about by forming or breaking intermolecular bonds. Studying these actions is the main topic of supramolecular chemistry.