In Windows 95 (MS-DOS 7.0) through Windows ME (MS-DOS 8.0), the DOS kernel has been combined with the DOS BIOS into a single file, IO.SYS (aka WINBOOT.SYS[2]), while MSDOS.SYS became a plain text file containing boot configuration directives instead.
Likewise, the MSDOS.SYS of the older system is named MSDOS.DOS for as long as Windows 9x is active.
This is the reason why a large dummy comment is typically found in the MSDOS.SYS configuration file since Windows 95.
The MS-DOS derivative Disk Control Program [de] (DCP) by the former East-German VEB Robotron used a DCDOS.SYS filename instead.
Windows NT-based operating systems (NT 3.1–4, 2000, XP, and 2003) use the NTLDR file and NT 6+ operating systems (Vista, 2008, 7, 8, 8.1, and 10) use bootmgr instead, as they have a different boot sequence.