From the New York Times obit:

In an interview in April with The New York Times, Ms. Politkovskaya said she had evidence of torture in Chechnya by Mr. Kadyrov’s police and other gunmen, including at least one witness who had been tortured by Mr. Kadyrov himself. Mr. Kadyrov has always vigorously denied such allegations.

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From the Novaya Gazeta site (RUS):

We do not know today who killed her and what for. We can only mention two main versions. Either this was the revenge of Ramzan Kadyrov, about whose activities she wrote and spoke a lot. Or it was done by those who want the suspicion to fall on the current Chechen premier, who, having turned 30, may aspire for the president's post.