Chromosomal instability (CIN) is characterized by an increased frequency of changes in chromosome structure or number and is regarded as a hallmark of cancer. CIN plays a prevalent role in tumorigenesis and cancer progression by assisting the cancer cells' phenotypic adaptation to stress, which has been tightly linked to therapy resistance and metastasis. Both, CIN-inducing and CIN-repressing agents are being clinically tested for the treatment of cancer to increase CIN levels to unsustainable levels leading to cell death, or to decrease CIN levels to limit the development of drug resistance, respectively. Noncoding RNAs (ncRNAs) including micro RNAs (miRNAs) and long noncoding RNAs (lncRNAs) have been fundamentally implicated in CIN. The miR-22, miR-26a, miR-28, miR-186 target important checkpoint proteins involved in mediating chromosomal stability and their expression modulation has been directly related to CIN occurrence. LncRNAs derived from telomeric, centrosomal and enhancer regions play an important role in mediating genome stability, while specific lncRNA transcripts including Ginir, GUARDIN, CCAT2, PCAT2, and NORAD have been shown to act within CINassociated pathways. In this review, we discuss how these ncRNAs either maintain or disrupt the stability of chromosomes and how these mechanisms could be exploited for novel therapeutic approaches targeting CIN in cancer patients.