Many of the important population centres have non-Greek names or names formed by attaching Greek suffixes to an opaque root.

Examples are:
Mycenae, Corinth, Salamis, Larissa, Olympus.

These non-Greek toponyms, hydronyms and oronyms appear in central-south Greece. They are lacking in Epirus where the archaic onomastic material is derived from proto-Greek. This supports the proposition that the proto-Greek developed in Epirus and that the Greek language was spread from this core area to cover the entire peninsula starting in the third millennium B.C.E.

Several of the figures appearing in Greek mythology have non-Indo-European names.

Examples are:
Odysseus, Achilles, Theseus, Athene, Aphrodite, Hermes

Greece, like Anatolia, does not share the "common Indo-European network" of ancient river names.

Place-names using the suffix "assos" and "os" may indicate the presence of an Indo-European substrate language among the non Indo-European substrates. These suffixes may derive from Luvian suffix "sas" (his/its) used in place of a genitive case. Luvian is an Indo-European language attested in western and south-western Anatolia from around 1900 B.C.E.

Examples are:
Parnassus, Knossos, Phaistos, Tylisos