At one time all were Orthodox Christians. It has always been about religion...especially in the Balkans.
Both are descendants of the same south slavic tribes that fell into different spheres of religiousity.
But no, they were not "all Orthodox" -- unless by "Orthodox" you mean the united Church before 1054. If you mean that, then I agree with you. If you mean Eastern Orthodoxy specifically in terms of following the Greek rite, then historically you are wrong -- from a Christian point of view that doesn't matter, yes, but historically, to be very specific, the South slavs were converted by missionaries both from Byzantium and from Rome -- in the 870s both the "proto Croats" and "proto Serbs" were converted by west and by east respectively.
however, over the next few centuries, Croatia united with the Hungarians and then Austrians while Serbia fell under Byzantine and then Ottoman rule.
They are still similar, but the nation is split by 1000 years of history.