Restriction endonucleases that recognize the same sequence are isoschizomers. The first example discovered is called a prototype and all subsequent enzymes that recognize the same sequence are isoschizomers of the prototype. The list below contains isoschizomers for commercially available restriction endonucleases. It also specifies which isoschizomer is available from New England Biolabs.

All recognition sequences are written 5´ to 3´ using the single letter code nomenclature with the point of cleavage indicated by a "/".

Numbers in parentheses indicate point of cleavage for non-palindromic enzymes. For example, GGTCTC(1/5) indicates cleavage at:
5´ ...GGTCTCN/...3´
3´ ...CCAGAGNNNNN/...5´

Isoschizomers with alternative cleavage sites are indicated with a " ^ ". Enzymes that are not currently commercially available are indicated with a " x ".

Neoschizomers are a subset of isoschizomers that recognize the same sequence, but cleave at different positions from the prototype. Thus, AatII (recognition sequence: GACGT↓C) and ZraI (recognition sequence: GAC↓GTC) are neoschizomers of one another, while HpaII (recognition sequence: C↓CGG) and MspI (recognition sequence: C↓CGG) are isoschizomers. Analogous designations are not appropriate for MTases, where the differences between enzymes are not so easily defined and usually have not been well characterized.

| A | B | C | D | E | F | G | H | I | K | L | M | N | O | P | R | S | T | U | V | X | Z |