Yeast species from the Lachancea genus belong to a phylogenetic clade within the Saccharomycetacae that was established before the ancestral whole genome duplication event that molded the genomes of Saccharomyces species. The 11.3 Mb genome of Lachancea (Saccharomyces) kluyveri displays an intriguing compositional heterogeneity: a region of ca. 1Mb, covering almost the whole left arm of chromosome C (C-left), has an average GC content of 52.9%, significantly higher than the 40.4% global GC content of the rest of the genome. This region contains the MAT locus, which remains normal in composition. The excess of GC base pairs affects both coding and non-coding sequences, and thus is not due to selective pressure acting on protein sequences. It leads to a strong codon usage bias and alters the amino acid composition of the proteins encoded on C-left. The 457 genes on C-left do not show obvious bias for functional categories, presence of paralogs or orthologs of essential genes of S. cerevisiae. They share significant synteny conservation with other species of Saccharomycetaceae, and phylogenetic analysis indicates that this chromosomal arm originates from a Lachancea species. In contrast, there is a complete absence of transposable elements in C-left, whereas 18 elements per Mb are distributed across the rest of the genome. Comparative hybridization of synchronized cells using high density genome arrays reveals that C-left is replicated later during the S-phase than the rest of the genome. Two possible primary causes of this major compositional heterogeneity are discussed: an ancient hybridization of two related species with very distinct GC composition, or an intrinsic mechanism, possibly associated with the loss of the silent cassettes (HML and HMR) from C-left that progressively increased the GC content and generated the delayed replication of this chromosomal arm.