The tandemly repeated ribosomal DNA (rDNA) multigene family (MGF) contains the transcription unit of the 45S ribosomal RNA (rRNA) precursor alternating with an intergenic spacer (IGS) that frequently contains iterated regulatory elements. Although the rRNA coding sequences are highly conserved, the IGS displays the high rates of interspecific sequence divergence typical of noncoding DNA. Homogeneity among rDNA copies within species, despite their divergence between species (concerted evolution) is influenced by the relationship between rates of mutation and rates of recombination among misaligned repeats during gene conversion and unequal crossing over. To determine the influence of repeat characteristics on their sequence divergence, I analyzed patterns of nucleotide variation in repeat arrays from 32 arthropod IGS sequences from eight families in the classes Branchiopoda and Insecta. I established that mean sequence divergence is lower among tandem repeats than among interleaved or dispersed repeats. I also demonstrated that longer arrays and longer repeats, as well as the presence of a TATA motif, positively affect the homogeneity of repeat arrays. In addition, I used phylogenetic footprinting methods to analyze these IGS sequences and identified five major conserved noncoding regions that are candidate regulatory elements. Finally, I identified patterns of recombination and/or homogenization within IGS subrepeat arrays in 13 complete IGS sequences from individuals of four species in the 'Daphnia pulex' complex and did not find a clear pattern of concerted evolution until after ~4 million years of divergence. Although homogenization can erase differences among repeat copies, copy number variation between homologous arrays is clear evidence that frequent recombination occurs within the IGS. I confirmed that terminal repeats in IGS repeat arrays evolve independently of the highly recombinagenic interior repeats, which tend to evolve in concert. The inclusion of interspecific hybrids in my analysis provided evidence that both inter- and intrachromosomal recombination occurs along the entire length of the IGS, with 5' to 3' polarity. Variations in the evolutionary trajectories of different IGS regions indicate that both genetic drift and natural selection influence the evolution of this region of the genome.