Isoschizomers are pairs of restriction enzymes specific to the same recognition sequence and cut in the same location. For example, Sph I (CGTAC^G) and Bbu I (CGTAC^G) are isoschizomers of each other. The first enzyme to recognize and cut a given sequence is known as the prototype, all subsequent enzymes that recognize and cut that sequence are isoschizomers. Isoschizomers are isolated from different strains of bacteria and therefore may require different reaction conditions.

An enzyme that recognizes the same sequence but cuts it differently is a neoschizomer. Isoschizomers are a specific type (subset) of neoschizomers. For example, Sma I (GGG^CCC) and Xma I (G^GGCCC) are neoschizomers (not isoschizomers) of each other.

An enzyme that recognizes slightly different sequence, but produces the same ends is a isocaudomer.

Isoschizomers are pairs of restriction enzymes which can recognize the same restriction site. But, out of the pair only one can recognize both the methylated as well as unmethylated forms of restriction sites. Whereas the other restriction enzyme can recognize only the unmethylated form of the restriction site. This property of the isoschizomers enables to identify the state of methylation of the restriction enzyme while isolating it from a baccterial strain. Example, restriction enzymes HpaII & MspI are isoschizomers, they both recognize the sequence 5'CCGG3' when it is unmethylated. But when the second C of the sequence is methylated only MspI can recognize both the forms while HpaII cannot.

de:Isoschizomer pl:Izoschizomery