Lloyds Banking Group said a Yes vote in the referendum is one of seven key risks ahead in its latest annual report, a list which also includes a raft of UK Government, European and international reforms and developments.
In its annual report, Barclays said that the referendum on Scottish independence in September 2014 and on UK membership of the European Union, expected before 2017, could affect the group's risk profile.
The Lloyds' report states: "The impact of a Yes vote in favour of Scottish independence is uncertain. The outcome could have a material impact on compliance costs, the tax position and cost of funding for the group."
Lloyds will continue to monitor the potential impact of a vote in favour of Scottish independence on the group's business and customers, the report said.
A UK Treasury spokesman said: "Lloyds have now joined RBS and Standard Life in reasonably and fairly pointing out the risks and costs that arise from independence.
"This uncertainty is made worse by the Scottish Government's failure to set out a plan for what currency it would use in the event of independence."
Scottish Conservative finance spokesman Gavin Brown said: "A clear pattern is now emerging, with increasing numbers of financial service companies having serious concerns about the uncertainty caused by the referendum."
Scotland's Finance Secretary John Swinney said: "Scotland has a strong and diverse economy and the point of independence is to win the powers we need to build on those strengths."