In a laboratory study, we investigated the clearance rates (CRs), respiration rates (RRs), total hemocyte count (THC), pathological alterations, and mucocyte densities in the gills of the short-neck clam Ruditapes philippinarum when exposed to the toxic dinoflagellate Heterocapsa circularisquama. Within 2 h of exposure to H. circularisquama at a concentration of 5–103 cells/mL, both the CRs and the RRs were significantly decreased by 43–52% compared with the control CRs and 43–93% compared with the control RRs, respectively (ANOVA, Newman-Keuls, P < 0.05). Clams exposed to H. circularisquama at 103 cells/mL for 96 h showed a set of defensive and degenerative pathologies that were absent in control clams. Within 3 h, the gills exhibited cilia matting, followed within 24 h by heavy hemocytic infiltration in the connective tissue of plicae, distortion of filaments, hyperplasia, and fusion of adjacent filaments with matted cilia. Within 48 h, the gill plicae became contracted and showed multifocal epithelial hyperplasia, increased filament fusion, exfoliation of the frontal cilia, epithelial desquamation, and abnormal epithelial masses. After 72 h, the gills presented extensive necrosis of epithelial and connective tissues, atrophy and fusion of the filaments, large masses of gill debris and mucus, and extensive exfoliation and loss of the frontal, laterofrontal, and lateral cilia. After 96 h, the gills of moribund clams exhibited more advanced stages of necrosis and degeneration. Quantitative analysis of the pathological alterations showed that both the prevalence and intensity of the defensive pathologies increased significantly, reaching their maximal values after 24 h of exposure, then decreasing. Meanwhile, the prevalence and intensity of the degenerative pathologies continued to increase throughout the experiments (ANOVA, Newman-Keuls/Fisher's LSD, P < 0.05). In addition, significant decreases in the THC (t-test, P < 0.01) and the total, acid, and mixed mucocyte densities in the gills (ANOVA, Fisher's LSD, P < 0.05) were observed after 48 h of exposure. The current study clearly showed physiological, pathological, and defense alterations induced by H. circularisquama in clams, highlighting the occurrence of cytotoxicity and tissue repair failure. Inhibition of feeding and respiration as well as extensive necrosis in the gills, coupled with depression of defense mechanisms resulting from depletion of hemocytes and mucocytes, ultimately resulted in the death of the clams.