限制修饰系统（英语：Restriction modification system）是一种存在于细菌（可能还有其他原核生物），可保护个体免于外来DNA（如噬菌体）的侵入。有些细菌体内含有限制酶，可将双股DNA切断，之后其他的内切酶再将切下的片段降解，因此能将入侵的外来DNA摧毁。

有些病毒则演化出对抗此系统的机制，它们的DNA经过了甲基化或糖基化的修饰，可阻碍限制酶的作用。另外还有一些病毒，如T3及T7噬菌体，则合成出一些可抑制限制酶的蛋白质。而为了进一步对抗病毒，有些细菌演化出专门辨识并切割已修饰DNA的限制系统。

The restriction modification system (RM system) is used by bacteria, and perhaps other prokaryotic organisms, to protect themselves from foreign DNA, such as that borne by bacteriophages. It was first discovered by Salvatore Luria and Mary Human in 1952 and 1953. They found that bacteriophage growing within an infected bacterium could be modified, so that upon their release and re-infection of a related bacterium the bacteriophage’s growth is restricted (inhibited) (also described by Luria in his autobiography on pages 45 and 99 in 1984). In 1953, Jean Weigle and Giuseppe Bertani reported similar examples of host-controlled modification using different bacteriophage systems. Later work by Daisy Dussoix and Werner Arber in 1962 and many other subsequent workers led to the understanding that restriction was due to attack and breakdown of the modified bacteriophage’s DNA by specific enzymes of the recipient bacteria. As reviewed by Daniel Nathans and Hamilton O. Smith in 1975, this work resulted in the discovery of the class of enzymes now known as restriction enzymes. When these enzymes were isolated in the laboratory they could be used for controlled manipulation of DNA, thus providing the foundation for the development of genetic engineering. Werner Arber, Daniel Nathans, and Hamilton Smith were awarded the Nobel Prize in Physiology or Medicine in 1978 for their work on restriction-modification.