3

From my dictionary, both mean ancestor so I am wondering about what is the difference between them.

Is the difference in politeness ? For example [息子]{musuko} and [子息]{shisoku} both mean son, but the latter is more polite.

5

Although both are on-yomi compounds, I feel 祖先 sounds more technical and academic. 先祖 tends to be used in daily conversations and religious contexts (e.g. 墓参り), whereas 祖先 tends to be preferred in biological, archaeological and programming contexts. This I think is why we commonly say ご先祖様 with respect but not ご祖先様. That said, this distinction is not very strict, and there are cases where 先祖 and 祖先 are used interchangeably.

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