We study the (p,q)5-brane dynamics from the viewpoint of
Matrix string theory
in the T-dualized ALE background.
The most remarkable feature in the (p,q)5-brane
is the existence of ``fractional string'',
which appears as the instanton of
5-brane gauge theory.
We approach to the physical aspects of fractional string
by means of the two types of Matrix string probes: One of which is that
given in Witten (New ``gauge'' theories in six dimensions,
JHEP01(1998)001 [hep-th/9710065]).
As the second probe we present
the Matrix string theory describing the fractional string itself.
We calculate the moduli space metrics
in the respective cases and argue on the specific behaviors
of fractional string.
Especially, we show that the ``joining'' process of fractional strings
can be realized as the transition from the Coulomb branch to the Higgs
branch of the fractional string probe.
In this argument,
we emphasize the importance of some monodromies related with
the θ-angle of the 5-brane gauge theory.