Massekhet Makkot appears immediately after Massekhet Sanhedrin, and effectively completes it. In contrast with the first tractates in Seder Nezikim (the Order of Damages in the Mishna) whose focus is on civil law, both Sanhedrin and Makkot deal with issues of criminal law and the punishments meted out by the courts in response to individuals who transgress Torah law. While Massekhet Sanhedrin dealt with severe crimes, including those where capital punishment was the appropriate sentence, Massekhet Makkot – as its name indicates – focuses on less severe crimes, whose punishments are less harsh.
The first Mishna in Massekhet Makkot deals with a situation of edim zomemin – false witnesses whose testimony will condemn the accused to receive punishment, even though they could not have been at the scene of the incident, given that others testify that these witnesses were with them in another place at the time that the crime took place. According to the Torah (see Sefer 19:15-21), the punishment for edim zomemin is that they will receive the punishment that would have been given to the defendant based on their testimony. Our Mishna teaches that this is not always the punishment that is given. In cases where the false testimony accused the defendant of something that would change his personal status – e.g., having questionable parenthood – we would not change the personal status of the edim zomemin, rather they would receive lashes as a punishment.
The Ritva asks why Massekhet Makkot begins with an analysis of edim zomemin rather than the laws of malkot that appear to be the central concept of the tractate, which do not appear until the third perek. The obvious answer – that is hinted to in the Gemara – is that this Mishna is the continuation of the Mishnayot in Massekhet Sanhedrin where the various punishments of the Jewish courts are discussed, and the law of edim zomemin is mentioned at the end of the tenth chapter (see Sanhedrin daf 84 where we learned that in many versions of the Talmud, that chapter was at the very end of Massekhet Sanhedrin).
Some even suggest that originally Massekhet Makkot was part of Massekhet Sanhedrin and that they were only separated at a later date.