The isochore theory became one of the most useful theories in molecular evolution for many years. It was the first and most comprehensive attempt to explain the long-range compositional heterogeneity of vertebrate genomes within an evolutionary framework. Despite the interest in the early years in the isochore model, in recent years, the theory’s methodology, terminology, and predictions have been challenged.
Because this theory was proposed in the 20th century before complete genomes were sequenced, it could not be fully tested for nearly 30 years. In the beginning of the 21st century, when the first genomes were made available it was clear that isochores do not exist in the human genome
nor in other mammalian genomes. When failed to find isochores, many attacked the very existence of isochores.
 The most important predictor of isochores, GC3 was shown to have no predictable power 
 to the GC content of nearby genomic regions, refuting findings from over 30 years of research, which were the basis for many isochore studies. Isochore-originators replied that the term was misinterpreted 
 as isochores are not "homogeneous" but rather fairly homogeneous regions with a heterogeneous nature (especially) of GC-rich regions at the 5 kb scale, which only added to the already growing confusion. The reason for this ongoing frustration was the ambiguous definition of isochores as long and homogeneous, allowed some researchers to discover "isochores" and others to dismiss them, although both camps used the same data.
The unfortunate side effect of this controversy was an "arms race" in which isochores are frequently redefined and relabeled following conflicting findings that failed to reveal "mosaic of isochores." The unfortunate outcomes of this controversy and the following terminological-methodological mud were the loss of interest in isochores by the scientific community. When the most important core-concept in isochoric literature, the thermodynamic stability hypothesis, was rejected, the theory lost its appeal. Even today, there is no clear definition to isochores nor is there an algorithm that detects isochores. Isochores are detected manually by visual inspection of GC content curves , however because this approach lacks scientific merit and is difficult to replicate by independent groups, the findings remain disputed.