The south Wales club sacked Brian Laudrup this week after a poor run of form saw them slide towards the relegation zone.
Garry Monk has been placed in temporary charge and is among the contenders for the permanent post, alongside Everton assistant Jones.
The 43-year-old was Martinez's right-hand man at Swansea between 2007 and 2009 before following him to Wigan and now Everton.
The Telegraph claimed earlier this week, prior to Laudrup's dismissal, that Jones was once again in the frame after discussions about the role in 2009 and 2010.
When asked about the links in his pre-Spurs press conference Martinez was keen to play them down, though there was no flat out denial either.
It's nothing new. Graeme and I have been working together since 2007 and it's good when you get those links because it means people still remember the work that you did at a previous club.
But Graeme is fully focused at Everton and it's not even a question.
The only thing that matters is the results at Everton and there's not going to be any changes in that respect.
Given the type of guy Martinez is I doubt he would stand in the way if Jones was offered the job at the Liberty Stadium.
However, it would cause unnecessary disruption at a crucial stage of the season, with Everton still battling on two fronts.
Interim boss Monk has already spoken of his desire to take the job permanently and a few good results would certainly help his cause.
The Swans board are already very jittery about relegation though after their costly sacking of Laudrup and may seek a quick external appointment if the team continue to lose matches.
Lets hope that whatever happens it has minimal impact on the Blues' plans for the second half of the season.