The markers display the White and Red Rose emblems of the Houses of York and Lancaster and are near the village of Ripponden, near Halifax.
They are among six buildings and monuments nationally selected and approved by Historic England, and all have ties to the Queen, who opened the M62 in 1971.
The boundary stones are being given Grade II-level protection.
The listings aim to highlight some of the many important places from Her Majesty’s reign and reflect the important social, technical and cultural changes which have taken place over the past 70 years, with those chosen marking different points in those years.
Historic England chief executive Duncan Wilson said: “These new listings celebrate the diversity and richness of our heritage overseen by Her Majesty during her 70-year reign, showing how the fabric of the nation has changed and developed.”
Construction on the M62 ended in 1970 with the completion of the final stretch through the Pennines.
The new motorway opened to traffic in 1971 and became the country's highest, reaching a summit of 372m across the Yorkshire-Lancashire border.
It was officially opened by Queen Elizabeth, and two plaques on pyramidal marker stones were constructed in commemoration of the achievement, one on each side of the M62, which runs through the two counties.
In place of county names, the markers instead display the historic symbols of the White Rose of the House of York and the Red Rose of the House of Lancaster; as well as highly recognised emblems of the two historic counties, the rose motifs are a reminder of the historic rivalry between the two, and the later uniting of the flowers by the house of Tudor.
The markers further reference the motorway’s surroundings through the use of local Pennine aggregate and stone in their construction.