物理马尔可夫链通常用来建模排队理论和统计学中的建模，还可作为信号模型用于熵编码技术，如算术编码（著名的LZMA数据压缩算法就使用了马尔可夫链与类似于算术编码的区间编码）。马尔可夫链也有众多的生物学应用，特别是人口过程，可以帮助模拟生物人口过程的建模。隐蔽马尔可夫模型还被用于生物信息学，用以编码区域或基因预测-Physical Markov chains are typically used to model queuing theory and statistics in modeling, but also as a signal model for entropy coding techniques such as arithmetic coding (famous LZMA data compression algorithm on the use of Markov chain and similar in arithmetic coding interval encoding). Markov chains also have many biological applications, particularly population processes, can help the process simulation modeling biological populations. Hidden Markov models are also used bioinformatics to the coding region or gene prediction