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<i>Mactra antiquata</i> sensu lato, a commercially important clam species in China, exhibits remarkable morphological and molecular diversity, which has led to the proposal of cryptic species within this complex. In the present study, specimens of <i>M. antiquata</i> sensu lato were collected from four coastal provinces (Shandong, Guangdong, Guangxi, and Hainan) of China, and an integrated comparative analysis was performed based on morphological traits and partial sequences of two mitochondrial genes (cytochrome c oxidase subunit I, <i>COI</i>; and <i>16S</i> rRNA). Our results revealed that <i>M. antiquata</i> sensu lato could be clearly delineated into two distinct clades: the N-group (comprising specimens collected from Shandong in this study) and the S-group (including specimens collected from Guangdong, Guangxi, and Hainan), with significant intergroup differences. Morphologically, S-group individuals possessed relatively narrower shells (mean shell width-to-length ratio = 0.465) and shorter shells (mean shell height-to-length ratio = 0.781) compared to N-group conspecifics. Additionally, the pallial sinus of S-group clams extended directly toward the anterior adductor muscle, whereas that of N-group clams pointed to the region below the anterior adductor muscle. Furthermore, the escutcheon of N-group individuals was considerably more slender than that of the S-group. Phylogenetic trees and haplotype networks constructed based on both partial <i>COI</i> and <i>16S</i> rRNA sequences further confirmed a deep genetic divergence between the two groups, with Kimura 2-parameter distances of 0.158 for <i>COI</i> and 0.084 for <i>16S</i> rRNA. Collectively, these morphological and molecular lines of evidence strongly support the existence of cryptic species within <i>M. antiquata</i> sensu lato. By comparing the morphological characteristics of specimens in this study with the original description of <i>M. antiquata</i>, we herein propose that the S-group represents a new species, which we named <i>M. haiboensis</i> sp. nov. Our findings provide a scientific basis for the targeted conservation and further research of both <i>M. antiquata</i> and <i>M. haiboensis</i> sp. nov.