はるかな昔。。。
マナの九によって進化した文明日が
地上とさかえていた
This does not make much sense. Are you sure there are no typos? Could it be マナの力 instead of マナの九? 文明日 is not a word. Could it be just 文明 without the 日? The last part also sounds strange. Let's assume it's a typo and it really is 地上
に さかえていた.
マナの力 (The power of MANA) によって (by) 進化した (evolved) 文明 (Civilization)が、地上に (above ground) さかえていた (was flourishing / thriving)。
I cannot imagine the verb さかえる not in your dictionary, though. Anyway, assuming my guess was close to the original sentence, the translation reads like this :
A civilization that had evolved by the power of MANA was flourishing above ground.
Now, if there was a missing comma between 文明 and 日, it would be possible that 日 is the name of the civilization.
Where is this from? Sounds like a passage from either a SF novel or a manga. If your Japanese is at the beginner's level like you wrote, maybe trying a different kind of material (a children's story, perhaps?) would be better.
Anyway, double check your source and try to type it exactly the way it appears in it so I or someone can tell you for sure what it means.