The invention relates to an isoprene oligomer that contains a trans structural moiety and a cis structural moiety, which can be represented by the following formula (1), wherein at least 1 atom or group in the trans structural moiety is replaced by another atom or group. The invention also relates to a polyisoprene, which is biosynthesized using the isoprene oligomer and isopentenyl diphosphate. Further, this invention provides a rubber composition comprising the isoprene oligomer and/or the polyisoprene, and a pneumatic tire, including tire components (e.g., treads and sidewalls) formed from the rubber composition. wherein n represents an integer from 1 to 10; m represents an integer from 1 to 30; and Y represents a hydroxy group, a formyl group, a carboxy group, an ester group, a carbonyl group, or a group represented by the following formula (2):