Large-scale micropropagation of sugarcane using temporary immersion bioreactors (TIB) holds several advantages, such as produces high-yields, and lowers explants exposure to growth hormones in media which may affects the frequency of somaclonal variation (SV) in the micropropagated plants. In this study, simple sequence repeat (SSR) analysis was conducted to determine the relative genetic stability of TIB-derived sugarcanes using 15 SSR markers (producing over 200 DNA fragments ranging from 150 to 4,000 bp in size). The genetic stability was calculated as the Jaccard’s similarity index of the SSR patterns of TIB-derived sugarcanes compared to their conventionally-propagated counterparts. The genetic stability varied between 92% to 96% in three Indonesian sugarcane varieties (PSKA 942, PS 094, and PS 091) which is relatively high considering the high cell mass multiplication in TIB (up to 30 multiplies). Morphological observations also revealed no difference between TIB-derived sugarcanes and their mother plants, convincing the true-to-type of micropropagation products. This study demonstrated the high relative genetic stability of TIB-derived sugarcanes, opening the possibility for large-scale commercial application for plantations.