EBay is not eBay without PayPal, and the same appears to be true for Alibaba and Alipay, but with one major caveat: Alibaba doesn’t own Alipay anymore.

As Alibaba heads for an initial public offering, the role Alipay plays — and it is a confusing one — in the future of the “Chinese Amazon” appears to be crucial to Alibaba. To be sure, Alipay is no shrinking violet. In 2013, Alibaba said Alipay was the largest online third-party payment services provider in China by total payment volume. Last Nov. 11, for example, a “Singles Day” promotion generated settlements through Alipay of RMB36.2 billion (US$5.8 billion) on Alibaba’s Chinese retail marketplaces within a 24-hour period.

Alipay is one of Alibaba’s leading risk factors. Specifically, Alibaba says in its IPO filing with the Securities and Exchange Commission that “our ability to provide reliable and trusted payment and escrow services through our arrangements with our related company Alipay” is a key risk factor.

But this risk factor is complicated by the fact that Alibaba no longer owns Alipay, which it launched in 2004. In 2010, Alibaba sold Alipay to two investors to satisfy Chinese regulators.

Here’s where things get interesting. After reviewing the S-1, it is difficult to trace all the payments to and from Alibaba and Alipay. Here’s what we could parse:

• Alibaba pays Alipay to settle transactions made through Alibaba — at yearend 2013, Alibaba owed Alipay 659 million RMB ($105.8 million);
• Alibaba pays Alipay for “certain intellectual properties” and for “software” — last year Alibaba paid Alipay 277 million RMB ($44.5 million) for that;
• Alipay pays Alibaba “royalty fees and software technology service fees, as well as government grants,” to Alibaba — for the last nine months of 2013, that amount was 1,178 million RMB ($189 million) up 98.7% compared to the same period in 2012.

Alibaba is also giving some Alipay executives shares.

Suffice it to say, money is flowing back and forth between Alibaba and Alipay to the point where it is hard to get to a bottomline reconciliation between the two, at least from the S-1. Not that that matters. What matters is that Alipay continues to service Alibaba, and while there is no indication that it will not, any investor considering Alibaba’s IPO should be acutely aware of this risk factor.

Alibaba may also be encroaching on Amazon‘s territory in the U.S. with its acquisition of ShopRunner, which offers free two-day shipping on purchases from a number of sites.