Four cDNAs (cDNAs 1-4), 162, 338, 321 and 167 bp in size, that contain repetitive DNA sequences, were isolated from C. reinhardtii. cDNAs 1, 2 and 3 hybridized to multiple transcripts in poly A+ RNA. Each of the four repeat families is comprised of an extremely heterogeneous population of interspersed nuclear DNA sequences most of which are less than 0.5 kbp in size. A large number of restriction fragment length polymorphisms were uncovered by using cDNAs 1 and 2 as hybridization probes. cDNA2 was compared to two different genomic DNA sequences: the first sequence was complementary to a central 136 bases of cDNA2, which is bordered by a 15-bp imperfect direct repeat; the second sequence lacks a poly-dA tail, but is otherwise colinear along its entire length with cDNA2. This suggests that some members of the cDNA2 repeat family contain signals for polyadenylation. The majority of accumulated transcripts that hybridize to cDNA2 have the same 5'-3' orientation as cDNA2.