Franchisers Hajinder and Narinder Atwal are accused of failing to ensure their branch of Subway in Edinburgh’s Forrest Road was kept clean.
Mouse droppings are said to have been found in the customer seating area, the front servery and the kitchen of the shop.
A staff changing room, a cleaning cupboard, an electrical cupboard, a store room and a stairwell are also said to have been found with droppings.
Demestes beetles and beetle larval casings are also said to have been found in the front servery, according to court papers.
Mouse droppings and mouse urine were also found on a counter top in the food servery, claim prosecutors.
The two men, from Edinburgh, are also facing charges they failed to ensure that fittings and equipment food came into contact with was sufficiently cleaned or disinfected at a rate sufficient to avoid contamination.
It is also claimed there were holes in shop cupboards. Pipe works under the main wash up area of the premises and outside the fire exit, also had holes, the charges against them claim.
Mice were able to enter the shop as a result, it is alleged.
It is said the construction of the shop prevented good hygiene practices, including protection against contamination and pest control.
The alleged food hygiene crimes were said to have taken place on May 21 last year.
Hajinder Atwal, 38, and Narinder Atwal, 41, who are respectively secretary and director of the firm SS North Ltd, were not present at today’s brief hearing at Edinburgh Sheriff Court.
The firm is facing the same charges.
The case was continued without plea until later this month.