This dataset reports the composition of glycerol dialkyl glycerol tetraethers (GDGT) extracted from the Irene sediment core collected from González Fjord, Baker-Martínez fjord system (48°S, Chile). The GDGT fraction was analyzed following Kaiser and Arz (2016). The fraction was filtered and then analyzed by high performance liquid chromatography coupled with atmospheric pressure chemical ionization mass spectrometry (HPLC APCI-MS). The separation of individual GDGTs was performed on a Prevail Cyano column (Grace, 3 mm, 150 mm x 2.1 mm). The compounds were identified by single‐ion monitoring (SIM) with m/z 1022 (GDGT‐Ia), 1035 (GDGT‐IIa), 1050 (GDGT‐IIIa), 1290 (crenarchaeol and its isomer, cren′), 1296 (GDGT‐3), 1298 (GDGT‐2), 1300 (GDGT‐1) and 1302 (GDGT‐0).