There are mainly two versions of SSH protocol. The initial version was SSH-1, which was released in July 1995. In 2006, IETF (Internet Engineering Task Force) published RFCs for a revised version of the SSH protocol SSH-2 as the standard. The two versions of SSH, SSH-1 and SSH-2 are not compatible.
SSH-1 (Initial version of SSH )
The first version of SSH was SSH-1. SSH-1 was the initial version of SSH invented by Tatu Ylonen, at Helsinki University of Technology, Finland. The reason behind the invention of SSH-1 was a password sniffing attack at the University on a less secure protocol. Tatu Ylonen released the first version of SSH in July 1995, as a free protocol. Tatu Ylonen released a software product also, based on that protocol. Immediately Tatu Ylonen saw a surge in number of users of SSH protocol. By the end of 1995, there were totally 20,000 users for SSH. There are some serious security vulnerabilities with SSH-1.
SSH-2 (Standard version of SSH)
SSH2 was introduced in 2006 as a standard by IETF. SSH-2 has many significant improvements over SSH1. SSH-2 prevents many security vulnerabilities of SSH-1. SSH2 is a much more secure and efficient than SSH-1. SSH-2 supports SFTP, a secure version of FTP. The main point to note is that, SSH-1 and SSH-2 are entirely different protocols. SSH-2 was completely designed as new, from the scratch. SSH-2 is the most commonly used version of SSH protocol these days.
SSH-1.99 (Backward compatibility version of SSH)
SSH-1.99 was also published as a standard in 2006 as RFC 4253. As discussed earlier, SSH-1 and SSH-2 are not compatible with each other. The purpose of SSH-1.99 is to provide backward compatibility for SSH-2 with SSH-1.