Argulus siamensis is an economically important crustacean ectoparasite in freshwater aquaculture affecting the growth and production of Indian major carp species (IMCs) mainly Labeo rohita. Not much progress has been made in the prevention or control of argulosis. The limited biological information at molecular level of this species is one of the major constrains to address this problem. To generate the molecular level information, both male and female parasites were processed separately to generate reference transcriptome sequences by using single molecular real time (SMRT) sequencing technique in PacBio Sequel system. Both sexes of parasites were collected (50 numbers) separately and starved for 24 h, and processed for RNA extraction followed by isoform sequencing. A total of 28.62 GB IsoSeq data for male samples from two runs and 11.81 GB for female sample in three runs were generated. Total full length non chimeric clustered consensus isoforms for female was found to be 84,337 whereas for male it was 2,09,271. All isoforms sequence data was considered for homology search with uniprot protein database and ~56% of the transcripts were annotated. The maximum percentage of sequences in female group showed significant similarity with Zootermopsis nevadensis followed by Daphnia magna where as in case of male top hit distribution showed maximum similarity with Daphnia magna followed by Zootermopsis nevadensis in organism plot. Total transcripts were mapped in GO database depicting their functions in biological process, molecular function and cellular components for both sexes. The candidate coding regions were analysed to find out the orthogroups genes specific for male and female. A total of 115 species specific genes were identified (105 for male and 10 for female). Overall, the information of A. siamensis male and female, generated by this method provides resources for future investigations, particularly generating sequence information for efficient prevention strategies for this parasite.