UPDATE 2-Alpha shareholder concerned over Foundation deal

* Duquesne says concerns over Alpha-Foundation merger

* Duquesne has 8.31 pct stake in Alpha Natural Resources

* Alpha stock rises 8.8 pct; Foundation up 7.7 pct (Updates with more background, closing stock prices)

NEW YORK, July 16 (Reuters) - Coal miner Alpha Natural Resources Inc's (ANR.N) largest shareholder said on Thursday it has concerns about Alpha's proposed $1.5 billion all-stock acquisition of Foundation Coal Holdings Inc FCL.N.

In a filing with the U.S. Securities and Exchange Commission, Duquesne Capital Management said it was evaluating its position on the transaction.

The filing said Duquesne has "concerns about the proposed merger between the company and Foundation Coal Holdings," which was announced in May.

It gave no further details, nor elaborated on its concerns. There was no immediate comment from Alpha, Duquesne could not be reached and a spokesman for Foundation declined to comment.

Duquesne holds 8.31 percent of Alpha's outstanding common stock and is the company's largest shareholder, according to Reuters data.

Alpha stock closed up $2.26, or 8.87 percent, at $27.73 on the New York Stock Exchange after the filing. Foundation's stock rose $2.11, or 7.72 percent, to $29.44.