Snapper shrimp is a symbiotic organism usually hidden under the rocks, sponges and pen shells in the seagrass and coral habitats. The relationship study within snapper shrimp and pen shell was conducted from Merambong shoal, one of the biggest seagrass beds in peninsular Malaysia. A total of 40 individual pen shells were collected randomly and four species of pen shells were identified. 40 Anchistus custoides were found inhabiting symbiotically in the mantle cavity of the pen shell as solitary males and females and heterosexual pairs. Pen shell, Pinna bicolor and Atrina vexillum recorded the highest average SH 217.79±53.15 mm, SV 2.62±1.36 dm3 and SH 164.10-224.78 mm with the SV 1.18±0.43 dm3, respectively compared to the other species. The size of Anchistus custoides ranged from 15.00 to 20.00 mm in length and it was determined to be female due to the presence of eggs in the pleopods. The length of the cephalothorax and its length were highly related (rs=0.563, p≤0.01, N=40) and found wider in females. A little difference in size between the left and right chela in males of identical length was noticed, although the left chela is much bigger than the right. The significant relationship (rs=0.450, p≤0.01, N=40) between the pen shell length and shrimp (male-female) length revealed that the size of the shell is important to be hosted the snapper shrimp in the shell cavity.