Of course they’re the same stock and came to the Balkans, where they mixed with the local inhabitants as perhaps one group in the 6th and 7th centuries. There are historians who think that Srb and Hrvat were the names of two Indo-Iranian groups that gave their names to the Slavs that then became Serbians and Croatians, kind of like the Bulgars gave their name to the Slavs of the more southern Balkans, but were then absorbed into the population and Slavicized, or like the Scandinavian Varangians became the ruling class and gave the name Rus’ to what later became the first Russian polity to be centered at Kiev. It fits so many peoples’ founding myth — including Greek peoples like the Spartans and the Thebans — that outsiders with special, even magical, powers arrive and organize simple tribal groups into coherent city-states and polities, that those myths probably are remnants of real processes and events.
So yes, outsiders like the Greek sources you’re referring to, were writing at a time when both Serbs and Croats were only first converting to Christianity and conditions and identities were in a state of flux. For a while it almost looked like Bosnia or even the first Serbian kingdom of Raška was going to become Catholic; I know, it sends chills down my spine too. Soon afterwards, however, the Catholic-Orthodox division solidified the two as separate ethnic and political identities.
And it’s been turtles all the way since then.

Despite their sophistication and the super-human effort they made to engage with their neighbors instead of waging costly warfare, the Byzantines were not — due mostly to their snobbery — the sharpest tools in the shed about the peoples around them, especially when they called the Turks Persians and the Slavs Scythians because those were the exonyms established by Attic historiography for those who lived in either of those directions.
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