They face being fined up to £160,000 for killing the protected species and causing long-term environmental damage to the River Lyon in Perthshire.
Scotland is home to around half of the world's population of pearl mussels – listed as one of the most critically endangered molluscs globally.
English firm Shawater Ltd yesterday admitted being responsible for the death and injury of pearl mussels over the course of more than a year while working on the Inverinian Hydro Scheme.
Between September 3, 2009, and October 1, 2010, Shawater Ltd allowed its sub-contractors to build a pipeline, a ford and an access track "in a manner likely to cause pollution to the water environment". It failed to prevent suspended solids from entering the Inverinian Burn and River Lyon and those caused damage to the river bed which resulted in car- nage to the mussel population.
Alan Smith, 48, a director of sub-contractor A&C Construction, and Charles Kippen, 52, from Stanley, Perthshire, a director of Chic Kippen & Son, also admitted similar charges of killing and injuring pearl mussels.
Smith, of Crieff, also admitted a second charge relating to the impact of work being carried out on the Castles Estate Hydro Project at Dalmally, Argyll. He admitted that between August 4 and October 4, 2010, he carried out activity liable to cause pollution to the water environment by constructing a ford crossing.
Sentencing in the case was put off until next week at Perth Sheriff Court. Each charge can mean a fine of up to £40,000.
Reports prepared for the case said the damage caused by the work could take as long as 1000 years to restore to its previous condition. A source close to the case said: "This work was done in a totally haphazard manner which paid little or no heed to the environmental requirements of the site. The mussel population in the River Lyon was of major international significance and has simply been devastated as a result of the work."
The bed of the River Lyon became clogged with silt during the work programme and the juvenile mussels were unable to obtain enough oxygen from the water to survive.
Within the past year, Scottish Natural Heritage (SNH) launched a programme to help save the pearl mussel because of ongoing concerns about decreasing populations in Scottish waters. An SNH spokesman said. "Scotland contains many of the world's most important remaining populations. But there has been a dramatic decline in the number of rivers that continue to support freshwater pearl mussels.
"Over the past 100 years, more than one-third of the rivers that used to contain freshwater pearl mussels no longer do so. A further one-third only contain old freshwater pearl mussels, with no sign of reproduction. They are witness to our rivers' deteriorating status and need urgent conservation action."
Freshwater pearl mussels are similar in shape to common marine mussels but grow much larger and live far longer than their marine relatives. They can live for as long as 130 years.
The mussels can grow to the size of a human hand and thrive at the bottom of clean, fast-flowing rivers. They feed by drawing in river water and filtering out fine particles.
They occasionally contain a pearl and illegal pearl-fishing has been primarily responsible for massive declines in their numbers and range. However, as filter feeders they are also extremely vulnerable to water pollution and engineering work in rivers such as the construction of weirs or deepening of pools.