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Amazon is expanding its delivery partnership with Whole Foods by rolling out free delivery from the grocery chain to Prime members in San Francisco and Atlanta.

Orders that total at least $35 can be delivered within two hours for free through Amazon’s Prime Now service, or within one hour for an extra $7.99 fee. The selection available for delivery from Whole Foods stores includes “thousands of items across fresh and organic produce, bakery, dairy, meat and seafood, floral and everyday staples,” according to a press release, as well as alcohol in San Francisco.

The announcement comes less than a month after Amazon first announced a delivery partnership with Whole Foods in four launch cities: Austin, Cincinnati, Dallas and Virginia Beach.

And the move is another signal that Amazon is moving quickly to integrate Whole Foods into the regular shopping habits of Prime customers, who are the catalysts of Amazon’s e-commerce domination. Two weeks ago, Amazon announced that shoppers who pay with the Amazon Prime Visa card would start getting 5 percent back at Whole Foods.

The Whole Foods-Prime Now delivery expansion raises questions anew about the status of Whole Foods’ multiyear partnership with the delivery startup Instacart, which counted the natural grocery chain as its largest customer and still delivers orders from its stores. The delivery partnership between the two companies was believed to contain some exclusivity around the delivery of perishable foods, but Amazon’s own Whole Foods delivery offering includes some perishable goods.

Both Amazon and Instacart continue to blow off questions about how the two competing delivery programs are live simultaneously — which is frustrating but telling.

To me, that means one of three things is likely true: Instacart’s original deal with Whole Foods was not as airtight as the startup originally let on; Amazon has worked out an unannounced agreement with Instacart to amend its deal with Whole Foods; or Amazon is just doing what it wants and daring Instacart to start a legal battle.

Have the answer? Email me at jason@recode.net or text me on any secure messaging app at 917-655-4267.

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