Cassava peel is a by-product produced at large amounts in starch-based agro industries and could be a major feedstock for bioethanol in most of the Asian countries. In this work, we aimed to evaluate two fermentation strategies for bioethanol production from alkali-assisted hydrothermal pretreated cassava peel by thermotolerant Kluyveromyces marxianus MTCC 4139 strain. Initially, milled cassava peel was subjected to alkali-assisted hydrothermal pretreatment at different autoclaving temperatures (110°C − 130°C) and residence times (15 − 30 min) in the presence of different NaOH concentrations (0.25% −1.0% w/v NaOH). On subsequent enzymatic hydrolysis of pretreated cassava peel (1% NaOH at 120°C for 30 min) with different optimal enzyme loadings (α-amylase, glucoamylase and cellulase) showed maximum 670.58 ± 10.13 mg/g reducing sugar yield with 81.25% ± 3.20% saccharification efficiency. Furthermore, SHF (separate hydrolysis and fermentation) and SSF (simultaneous saccharification and fermentation) of cassava hydrolyzates were studied for improved ethanol yield and fermentation efficiencies. SSF of hydrothermal pretreated cassava hydrolyzate with K. marxianus strain showed higher ethanol yield (0.44 g/g) with 86.11% fermentation efficiency as compared to SHF process (0.41 g/g; 80.24% fermentation efficiency).