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.
2 Answers
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.
I'm 2 years late, but in case anybody stumbles upon this...
The meanings are pretty much the same, but the usage is pretty different.
先祖 is used colloquially, as in: 先月、ご先祖様のお墓参りに行きました。(I payed a visit to my ancestors' grave last month.) Note that you cannot use 祖先 here.
On the other hand, 祖先 is used almost exclusively in a scientific context. For example, 人類の祖先はアフリカで誕生したとする説が有力だ。(It is widely believed that Humans' ancestors originated in Africa.) You can not use 先祖 here.
