Macronuclear chromosomes in Oxytricha fallax, a hypotrichous ciliate, are very short. They often belong to small families of cross-hybridizing chromosomes of two or three different sizes. For example, the 81-MAC family consists of three sizes of macronuclear chromosomes (4.9, 2.9, and 1.6 kbp) (Cartinhour and Herrick 1984). We show that the family actually consists of two closely related sets of three each and that the two sets are independently created by alternative processing of two separate precursor (micronuclear) versions. Chromosomes of a set share a common 1.6-kbp region, which contains a transcribed gene coding for a 25-kD protein. Different-sized macronuclear chromosomes of a set result from alternative choices of positions for telomere formation. All six members of the family are reproducibly generated in each developing macronucleus, and their copy numbers are stably maintained during vegetative replication of the macronucleus (Herrick et al. 1987). Here we argue for the existence of three distinct copy control elements in the 81-MAC family chromosomes. A model is discussed in which, following polytenization of the micronuclear chromosomes, different chromatids are processed differently, and, subsequently, replication-competent macronuclear chromosome products are amplified under the influence of the vegetative copy control elements.