Genomes are compartmentalized in mosaics of fairly homogeneous stretches of DNA with distinct average GC levels. These regions, termed isochores, show differences in gene composition and expression patterns, DNA methylation abundance and overall chromatin structure, and were thereby proposed to provide an ancient level of genome organization. Sequencing of the Trypanosoma cruzi genome revealed two main isochoric regions: a GC-poor “core” compartment, displaying synteny with those of phylogenetically related organisms and a GC-rich “disruptive” compartment, comprising repetitive sequences and gene families involved in the parasite-host interplay. Despite their potential relevance, several limitations preclude the precise distinction of both compartments on the parasite genome, which is currently based on the presence/absence of diagnostic gene markers. Here we present GCanner, an interactive tool for genome-wide GC composition analysis. When applied to T. cruzi, it allowed for the accurate and unbiased identification of the “core” and “disruptive” compartments. Seamless integration of isochoric data with efficient genomic mapping and compartmental distribution of genes of interest provides novel insights into parasite genome organization and facilitates structural and functional genomic analyses.