Biodiversity is a measure of interest in many studies of global change. Depending on the question addressed, it takes a taxonomic, genetic, phylogenetic or functional perspective. Although aspects of morphology might be part of functional metrics, organism morphology is rarely considered explicitly in this context. We describe the changes in morphological diversity of marine zooplankton on the seasonal and long-term timescale. We digitalized weekly plankton samples collected from 2009-2020 in the NW Mediterranean Sea and automatically extracted 45 morphological features on > 800,000 individuals. Applying dimensional reduction (PCA) followed by clustering, we synthesized these features into four main morphological traits (describing size, transparency, circularity and shape complexity) and defined morphological groups (or ”morphs”). Based on these morphs, we computed time-series of morphological diversity indices (richness, divergence and evenness) relaying to metrics originally developed for functional diversity. Over the 12-year period, morphological – but not taxonomic – diversity increased while zooplankton concentration decreased. The environmental changes during this period consisted mainly in an increase in temperature and salinity and an overall impoverishment of surface waters, suggesting that niche specialization under low productivity increased the morphological divergence. Notably, an increased variability in the four morphological traits and higher proportions of extreme individuals caused this trend, with likely consequences for the ecosystem.