The spider-like strombid Lambis lambis is widely distributed in the Indo-Pacific region and possesses morphological diversity. In the present study, the complete mitochondrial genomes of two morphologically different specimens of L. lambis that were collected in Sanya (SY) and Zhaoshu (ZS) islands of the South China Sea (namely L. lambis-SY and L. lambis-ZS) were sequenced. They were also compared with that of L. lambis previously published and sampled from coastal waters of Quanfu (QF) Island of the South China Sea (namely L. lambis-QF). The newly sequenced mitochondrial genomes L. lambis-SY and L. lambis-ZS contained 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and several noncoding regions, indicating a similar pattern with respect to genome size, gene order, and nucleotide composition compared with that of L. lambis-QF. Although L. lambis-SY and L. lambis-ZS differed in shell morphology, the genetic distance between them was small. On the other hand, considerable genetic distance values were detected between L. lambis-QF and L. lambis-SY/L. lambis-ZS, suggesting that the former might be a possible cryptic species within L. lambis. The divergence of the cryptic lineage L. lambis-QF was dated to 4.6 Mya, falling in the lower Pliocene that corresponded to a paleoclimatic transition from cool to warm conditions. This study, therefore, suggests a correlation between paleoclimate change and speciation event.