markov count and rainflow count

Basic difference is rainflow does not assume all future information is contained in the present state. Also, rainflow can reduce a larger spectrum of data into sets or subsets, using software programs, one can do this apply Markov's principle but it requires more iterations.

The Rainflow count is used in the analysis of fatigue data in order to reduce a spectrum of varying stress into a set of simple stress reversals. Its importance is that it allows the application of Miner's rule in order to assess the fatigue life of a structure subject to complex loading.

The Andrey Markov count is a random process where all information about the future is contained in the present state, so one does not need to examine the past to determine the future. This might not be the case in your exact analysis, you need to decide. To be more exact, the count with the Markov property, means that future states depend only on the present state, and are independent of past states.