Temporal variation of hyperiid amphipod structure assemblages was studied on Isla Gorgona, eastern tropical Pacific (ETP) off Colombia between September 2005 and August 2006. Forty-six species were found during the entire sampling period: Hyperioides sibaginis, Lestrigonus bengalensis, Phronimopsis spinifera, Tetrathyrus forcipatus and Paralycaea gracilis dominated the assemblage, representing 92%. The dendogram based on the Bray–Curtis similarity index showed that the hyperiid assemblages were separated into two groups, which did not coincide with the seasonality described for the ETP (wet versus dry season). Rather, groups comprised wet (May to November) and dry season months (December to April). The first group included November, December, February and March. During these months, significantly higher hyperiid richness, diversity and abundance were found, although colder subsurface water temperatures in Gorgona were registered only during February and March. The other group included May to October and January, and was characterized by lower hyperiid diversity and abundance values. Significant correlations were found between hyperiid abundance and the possible gelatinous zooplankton hosts (medusae, siphonophores and salps). This study contributes to increasing knowledge of the zooplankton community in the Panama Bight, as well as of a poorly studied group in the ETP.