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Good question. It's because of the Sun's temperature. H-alpha is the line produced from exciting an electron from n=2 to n=3 level. Note that to be able to absorb H-alpha, you would need to have a hydrogen atom with its electron already in the n=2 excited state! Exciting n=1 to n=2 (Lyman-alpha) takes a lot of energy, much more than n=2 to n=3, and the Sun's photosphere is not hot enough for much of its hydrogen to be in the n=2 excited state. Hotter stars have more hydrogen in the n=2 state, so it is then easy to do the (less energetic) n=2 to n=3 H-alpha absorption. That's why hotter stars like A stars have much stronger H-alpha lines.

Note that stars hotter than A stars (O,B) again have weak hydrogen absorption lines, because they are so hot most of their hydrogen is ionized, and again there is not much hydrgoen in the n=2 state to excite.

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