The 1906 Jewish Encyclopedia [answers][1] that the division of the several treatises into chapters as well as the sequence of these chapters was the work of Rabbi [Yehuda HaNasi] himself although some changes were made over time. See [there][1] for full references.

> **The division of the several treatises into chapters as well as the
> sequence of these chapters was the work of Rabbi himself** (Letter of
> Sherira Gaon, l.c. p. 13). The portion discussed each day constituted
> an independent pereḳ; and this term was, therefore, applied elsewhere
> to a single discourse also. **Generally speaking, the original division
> and sequence of the chapters have been preserved**, as appears from
> various passages of the Talmud (R. H. 31b; Suk. 22b; Yeb. 9a; Ket.
> 15a; Niddah 68b; Zeb. 15a).
> 
> The names of the chapters taken from the initial letters are likewise
> old, and some of them are mentioned even in the Talmud (B. M. 35b;
> Niddah 48a). **In the course of time, however, various changes were made
> in the division, sequence, and names of the chapters**; thus, for
> example, the division of Tamid into seven chapters is not the original
> one. On other variations in sequence see Frankel, l.c. pp. 264-265,
> and on the changes in the names see Berliner in "Ha-Misderonah," i.
> 40b.


  [1]: http://www.jewishencyclopedia.com/articles/10879-mishnah#anchor14