On Wednesday morning we reported that Cisco, the owner of the “iPhone” trademark, was waiting for Apple to return a contract covering its usage of the brand. By late Wednesday night the deal appeared to have gone sour and Cisco has now set its legal team on the iPod maker.

In a statement released late Wednesday, Cisco said it had filed a lawsuit in the US District Court for the Northern District of California against Apple, “seeking to prevent Apple from infringing upon and deliberately copying and using Cisco’s registered iPhone trademark”.

Cisco obtained the “iPhone” trademark in 2000 through the acquisition of Infogear, which itself had applied for the trademark in 1996.

Linksys, another division of Cisco, has been shipping a family of wifi-enabled VoIP devices under the iPhone brand since early last year and added launched a handful of new iPhone devices in mid-December.

Given that Cisco and Apple have been in discussions over the “iPhone” trademark for some years, it could be that Cisco knew January was going to bring the big announcement and thought to get a few more of its own iPhone gadgets out a few weeks earlier.

“Cisco entered into negotiations with Apple in good faith after Apple repeatedly asked permission to use Cisco’s iPhone name,” said Mark Chandler, senior vice president and general counsel, Cisco. “There is no doubt that Apple’s new phone is very exciting, but they should not be using our trademark without our permission”.

Later on Wednesday Apple and networking giant Cisco are expected to announce an agreement on the Californian computer company’s licensing of the “iPhone” trademark.

Apple wowed the mobile world on Tuesday with the unveiling of the gadgety goodness that is the iPhone, Apple’s much hyped music player/web browser/phone combo.

But Cisco had rained on Apple’s parade just three weeks earlier, when subsidiary company Linksys launched a bunch of wifi phone devices under the “iPhone” brand.

Late Monday Cisco said that it had been in discussions with Apple for several years now over granting permission for the use of Cisco’s “iPhone” trademark.

The networking company said it expected to receive a signed agreement to the licensing document and public statement on Tuesday night. A further announcement is expected imminently.