The glorious Win-Tel alliance upon which the sun never set, appears to be crumbling from within, according to IHS iSuppli analyst Craig Stice.

He said in a report that the willingness of Intel and Microsoft to work together is also fraying as each company increasingly adopts strategies "that work against each other's interests. Stice claimed that the days of the pair marching shoulder to shoulder, dominating the PC market with their closely tied operating system and microprocessor technologies were fading.

The strategy has begun to change in visible ways during the mobile era. This is despite surface appearances that indicate once-mighty Wintel is still pretty mighty, actually.

But going forward and if current trends hold, both Microsoft and Intel stand to lose a good deal of their market share in operating systems and microprocessors, respectively, the analyst said. Wintel is expected to suffer a declining share of the 'new' computer market, a category consisting not just of PCs but also of the much faster-growing smartphone and media tablet segments," Stice added.

Microsoft had a 44 percent share of the OS market for PCs, tablets, and smartphones in 2011, according to IHS iSuppli. This could fall to a third in 2016, the research firm predicted. Intel's projected market share decline over that same period follows a similar line—from 41 percent of the global microprocessor market to 29 percent, according to IHS iSuppli.

If such a market share decline for Wintel does come to pass, however, it might not actually affect the numbers of units shipped by the two tech giants much at all. For example, IHS iSuppli forecast that the total size of the microprocessor market will double from 2011 to 2016, meaning Intel could lose a lot market share and still wind up moving more chips than ever.