In Drosophila, meiotic recombination is initiated by the formation of programmed DNA doublestrand breaks (DSBs), which occur within the context of the synaptonemal complex (SC). We created an in-frame deletion mutant in c(3)G (deleting amino acids L340 to N550, denoted as c(3)GccΔ1), which encodes the major transverse filament protein of the SC. Although c(3)GccΔ1 oocytes assemble full-length SC and exhibit normal DSB formation, euchromatic SC in both c(3)GccΔ1 heterozygotes and homozygotes precociously disassembles in early to mid pachytene. Centromeric SC, however, is unaffected in both genotypes. Thus, c(3)GccΔ1 is a separation-offunction mutant that establishes different functional and structural requirements between euchromatic and centromeric SC. Additionally, the chromosomes differ in their sensitivity to c(3)GccΔ1-induced perturbations in the SC. The X chromosome is distinctly sensitive to these perturbations, such that euchromatic pairing and crossing over are altered in c(3)GccΔ1 heterozygotes and severely reduced in c(3)GccΔ1 homozygotes. On the autosomes, crossovers are shifted to centromere-proximal regions and crossover interference is defective in both c(3)GccΔ1 homozygotes and heterozygotes. However, only c(3)GccΔ1 homozygotes display a progressive loss of euchromatic pairing in distal autosomal regions, suggesting that discontinuity in the euchromatic SC—rather than failed pairing—might cause the altered crossover distribution. These phenotypes reveal that different chromatin states or regions have differing requirements to maintain both the SC and homologous pairing. Furthermore, c(3)GccΔ1 is the first mutant in Drosophila to demonstrate that the SC appears to facilitate the regulation of recombination frequency and distribution differently on each chromosome.