The Chessie System began as an "affiliation" in 1963 when the C&O purchased the B&O railroad. Both railroads continued to operate independently with very few changes. The main reason for the continued separation was the long standing tax incentives held by the B&O. On the outside however, one would think the B&O had actually acquired the C&O. Both railroads had adopted the simplified blue and yellow scheme with logos on the ends and initials on the sides. The main difference was the C&O painted the front hood yellow. All letterheads showed the two logos side by side with the C&O logo slightly imposed over the B&O.

 No changes to equipment where made either. Both used their own numbering systems until 1964 when GP35s where purchased using the C&O's system of using the model number to designate the locomotive class. During 1966 and 1967 the entire roster was renumbered to a unified system, including the Western Maryland which was owned and controlled by th B&O. The Central of New Jersey and Reading where also controlled by the B&O at that time and had been renumbered in 1964 to avoid any conflicts. The CNJ had also adopted a similar blue and yellow scheme. With the purchase of SD40's in 1967, the yellow was dropped from the C&O units.

 In August of 1965 the C&O/B&O intended to merge with the N&W and further renumberings ocurred in both railroads, as well as the adoption of blue and yellow by the N&W. When merger talks ended in 1971 the N&W changed its scheme to black and white with simple NW lettering. When the C&O/B&O began merger procedings in 1971, the Reading petitioned to be included, but was unsuccessful. The WM which was already owned by the B&O was included. In 1972 the Chessie System paint scheme with the Chessie cat logo was adopted. The WM did not begin consolidation into the Chessie System until 1973 and continued to operate it's own sales department even after much of its mainline was considered redundant and abandoned. The WM continued to use the red, white, and black paint scheme until 1975 when a chop nosed GP9 was renumbered and painted in Chessie colors.

 The WM maintained its fleet of first generation Alcos and F Units until its shops in Hagerstown where closed in 1976 and repairs transfered to Cumberland, MD. Chessie did not maintain them with the same standards and operated them until trade-in or major failure. None of them were ever painted Chessie. With the loss of WM engines, many C&O GP9's where transfered to the WM, as the C&O often transfered older engines to the B&O. Many blue and yellow units only received a relettering of WM on the side. Other idle units where also leased to western railroads like the Santa Fe and received SF style Roman lettering in the 1980's. When C&O subsidiary Chicago, South Shore and South Bend received 10 new units, its blue and yellow C&O GP7's where returned and transfered to the B&O Chicago Terminal Railroad. The CSS&SB had renumbered them into the 1500's and they kept those numbers until the arrival of the GP15T's.

On November 1, 1980, Chessie System and Family Lines became the CSX Corporation, initially just a holding company. On January 1, 1983, Family Lines became Seaboard System, and new orders of SD50s where consolidated with the Chessie System numbers. As units received the Seaboard System paint and numbers they began losing their original identities. In 1986 the two companies began consolidation into the new CSX paint scheme ending the Chessie System era. The WM was merged into the C&O on May 1, 1983. The B&O was merged into the C&O on April 30, 1986. The C&O itself was merged into CSX Transportation on July 1, 1986. At that time over 75% of the Chessie System engines had been painted in Chessie colors. While numbers were allocated for first generation diesels in CSX, many were never painted or renumbered. Some GP9's received spray painted numbers, or simply had the first digit blanked out. CSX later chose not to repaint all of its second generation diesels, as they were soon to be retired. Some received the orange and black maintenance of way scheme. Now very few engines still operate in Chessie System paint and even fewer in blue and yellow.