The micronuclear genes encoding alpha-telomere-binding protein (alphaTP) in Oxytricha trifallax and Stylonychia mytilus contain multiple internal eliminated segments, or IESs, that divide the gene into multiple parts called macronuclear destined segments, or MDSs. The MDSs have become disordered, or scrambled, during evolution. The scrambled structures of the alphaTP genes in Oxytricha trifallax and S. mytilus have been compared with the previously published scrambled structure of the alphaTP gene in O. nova. The scrambled patterns of the alphaTP gene in the three species are similar but show significant differences. The micronuclear genes in O. nova and S. mytilus consist of 13 IESs and 14 MDSs, but the gene in O. trifallax is divided into three additional MDSs by the presence of three additional IESs, believed to have been inserted into the O. trifallax alphaTP gene after divergence of O. trifallax from the other two species. Corresponding IESs among the three species have shifted along the DNA during evolution, presumably by a mutational mechanism that changes the short repeat sequences that flank IESs. The IESs also have changed markedly in length by insertion and/or deletion of nucleotides. Comparison of the putative alphaTP amino acid sequences in the three species reveals three conserved and three nonconserved domains. The 5' nontranslated regions of the gene-sized molecules encoding alphaTP contain several conserved segments, and the 3' nontranscribed trailer contains one conserved segment.