Periclimenes rectirostris Bruce, 1981 and Periclimenes josephi Li, 2008 are two palaemonid shrimps reported from the deep water in the western Pacific. Prior morphological studies suggest their systematic status might be problematic. Therefore, we attempted to re-evaluate the systematic status of the two species in this study. Based on an analysis incorporating molecular, morphological and ecological data, P. rectirostris is suggested to belong to the genus Sandimenes Li, 2009, but the systematic status of P. josephi is still undetermined due to the polyphyletic state of the genus Zenopontonia Bruce, 1975a. Meanwhile, a preliminary reconstruction of the evolutionary process of the echinoid-associated palaemonid shrimps is presented. Additionally, a well-supported clade mainly comprising the echinoderm or mollusc-associated taxa is recovered, and multiple host shifts are presumed to have occurred during their diversification.