With its older E-units reaching the end of their serviceable lives, Seaboard Air Line asked EMD for a passenger version of the SD35 that could double as a freight unit, especially if passenger trains continued to be discontinued. EMD came up with the SDP35, and SAL placed an order, trading in E4 and E6 units. The first of SAL's new SDP35s was delivered in summer 1964. Eventually the SDP35 wound up going to four railroads: SAL, Atlantic Coast Line, Louisville and Nashville and Union Pacific. The SD35 and SDP35 were so similar that EMD published a single operator's manual to cover both. Although SAL successfully used the SDP35 in high-speed passenger service as well as on expedited freight and piggyback trains, Union Pacific found it unsuitable and relegated its entire fleet to freight service while its famous yellow E-units continued to handle passengers. With the July 1, 1967 Seaboard Coast Line merger, SAL units received passenger numbers 601-620 and also served SCL in both high-speed freight service and on passenger trains. With the arrival of Amtrak, SCL renumbered them into the freight series and numbers 1951–1970. Later in their SCL years, they were renumbered again and assigned into the heavy yard duty and assigned 4500-series numbers. ACL's lone unit was renumbered 1099 when the line acquired former MKTE8s. At the SCL merger, it was assigned number 600 and then later received SCL number 1950. Louisville & Nashville's four SDP35s, ordered in spring 1964 to replace aging E and F units in passenger service, were completed and delivered without steam generation equipment installed, after approval of several passenger train cancellations from government regulatory agencies during the locomotives' assembly, leaving L&N with a surplus of passenger locomotives. After delivery L&N assigned the SDP35s to general freight service, installing radio control locomotive equipment in the steam generator compartment and using the engines in locotrol service until 1969. In 1966, when the EMD 645prime mover superseded the EMD 567, the SDP35 was replaced in EMD's catalog by the EMD SDP40.
Former Seabord Air Line 1111 is the last operating SDP35 in its original carbody, as Southwest Portland Cement 411, now CEMEX, in Victorville, California.