In this study, heterochromatin distributions in the chromosomes of 11 small mammals of two different species (Chionomys nivalis and Apodemus agrarius) from four different localities of Turkey were investigated by using standard karyotype and C-banding method. Chionomys nivalis karyotype included 2n=54 chromosomes, NFa=52, X=submetacentric, Y=acrocentric. Apodemus agrarius karyotype included 2n=48 chromosomes, NF=56, X=acrocentric, Y=acrocentric. In this study, C-banding heterochromatin distribution in C. nivalis and A. agrarius karyotypes was reported for the first time in Turkey populations. In C. nivalis karyotype, autosomes and the X chromosome had slight centromeric positive C-bands and the Y chromosome was entirely C-positive. In A. agrarius karyotype, all chromosomes had C-band positive characteristics.