Branched glycerol dialkyl glycerol tetraethers (brGDGTs) are thought to be produced by as yet unknown bacteria on land, and their distribution in soils, peats, and lake sediments has been shown to correlate with mean annual air temperature (MAAT). Recently, an increasing number of studies have shown that in situ production of brGDGT in marine environments is likely. However, the influence of environmental factors on marine-derived brGDGT distributions is still unknown. In this study, we assessed the sources of brGDGTs preserved in a sediment core from the Chukchi Sea shelf using multiple brGDGT-based indices, including the branched and isoprenoid tetraethers (BIT) index, the ratio of IIIa/IIa, cyclization degree of branched tetraethers (CBT), and #rings indices, and discuss the influence of seawater temperature changes over the last 70 years on the distribution of brGDGT isomers. The low BIT and CBT values, high IIIa/IIa ratios, and significant correlations between different #rings indices suggest that these brGDGTs primarily have a marine source. With increasing sea surface temperatures (SSTs), the fractional abundances of 5-Me IIIa (IIIa5) showed an increased trend, while there was no obvious trend in 6-methyl IIIa (IIIa6). This finding indicates different behaviors of 5-Me and 6-Me isomers in marine-derived brGDGTs, similar to what has been observed in soils, peats and lakes. In addition, we found a significant correlation between IIIa5 and IIIa7 (a novel isomer of IIIa), indicating that they might share the same bacterial source and/or are controlled by the same environmental factors (e.g., temperature). Finally, the fractional abundances of IIIa5 and IIIa7 are significantly correlated with SST (r2 = 0.64 and 0.49, respectively), which suggests that marine-derived brGDGTs have the potential to reconstruct seawater temperature.