The record for plankton biomarkers in sediment trap samples from a one-year experiment in the central Arabian Sea (AS4: 15°59′N 61°30′E) shows variations that reflect changing biological conditions in surface waters. Particulate fluxes of C 37–39 alkenones, highly branched C 25 isoprenoids (HBI), dinosterol, nC 28 12-hydroxy fatty acid, 24-ethylcholesterol, and a C 30–34 series of pentacyclic triterpanols all displayed distinct maxima at the start and stop of the Northeast (NE) and Southwest (SW) Monsoons. Surface mixing conditions changed rapidly at these times, altering light and nutrient availability, thereby triggering these biomarker signals of export production. Temporal offsets noted in individual biomarker concentrations (per g total organic carbon) at the start of the SW Monsoon suggest succession occurs in the phytoplankton community contributing to organic matter export. Comparable offsets were neither apparent at the start of the less dynamic NE Monsoon nor at the end of the NE or SW Monsoons. Broad concentration maxima for HBI also were observed at the beginning and end of the time-series during the relatively quiescent Fall Intermonsoon period when such features were conspicuously absent for other biomarkers. HBI are reputed biomarkers of Rhizoselenia and Haslea spp., two recognized dominants of diatom biomass in the Arabian Sea. These peaks in biomarker concentration could reflect either changes in the relative proportion of specific organisms that contribute to the upper ocean productivity or enhanced preservation of the biomarkers during times of high export production. In either case, the biomarker record in sediment traps reflects important changes in the biological condition of the upper ocean. All biomarkers except HBI were measurable in surface sediments deposited beneath the trap site. Comparison with concentrations in average sediment trap particles showed each was sensitive to significant (∼99%) degradation, displaying depletion factors relative to TOC of ⩾4. Clearly, consequences of such high levels of early diagenetic recycling must be considered carefully when conclusions about changes in export production from surface waters in past oceans are drawn from stratigraphic analysis of biomarkers in marine sediments.