Coat colour and pattern are a distinguished feature in mammalian carnivores, shaped by climatic cycles and habitat type. It can be expressed in various ways, such as gradients, polymorphisms, and rare colour variants. Although natural selection explains much of the phenotypic variation found in the wild, genetic drift and heterozygote deficiency, as prominent in small and fragmented populations, may also affect phenotypic variability through the fixation of recessive alleles. The aim of this study was to test whether rare colour variants in the wild could relate to a deficiency of heterozygotes, resulting from habitat fragmentation and small population size. We present an overview of all rare colour variants in the order Carnivora, and compiled demographic and genetic data of the populations where they did and did not occur, to test for significant correlations. We also tested how phylogeny and body weight influenced the presence of colour variants with phylogenetic generalized linear mixed models (PGLMMs). We found 40 colour-variable species and 59 rare colour variants. In 17 variable phenotypic populations for which genetic diversity was available, the average AR was 4.18, HO = 0.59, and HE = 0.66, and FIS = 0.086. We found that variable populations displayed a significant reduction in heterozygosity and allelic richness compared to non-variable populations across species. We also found a significant negative correlation between population size and inbreeding coefficients. Therefore, it is possible that small effective size had phenotypic consequences on the extant populations. The high frequency of the rare colour variants (averaging 20%) also implies that genetic drift is locally overruling natural selection in small effective populations. As such, rare colour variants could be added to the list of phenotypic consequences of inbreeding in the wild.