Settlement is a key factor determining recruitment into the fishery in marine organisms. However, little is known about the processes driving settlement patterns due to the difficulties associated to tracking larvae in the ocean. An alternative to this problem is to use molecular markers in recently settled individuals in order to determine population of origin and level of kinship between settlers. The present study aims to investigate whether Jasus edwardsii settles in genetic cohorts and to examine the relationship between puerulus morphological attributes and genetic identity. Recently settled puerulus were collected in 2012 from three sites in Tasmania during three winter months. Samples were sequenced through five double-digest restriction site associated DNA sequencing (ddRADseq) libraries using the Illumina HiSeq platform. Demultiplexed reads were used to create a reference catalog of loci and individual reads were then mapped to the reference catalog and variant calling was performed. Kinship analysis revealed that a large proportion of pueruli had 2nd and 3rd degree relationship and a small proportion of samples were full siblings. Population structure was investigated through a Discriminant Analysis of Principal Components and identified two clusters among all locations and settlement pulses. A logistic model identified a negative relationship between DAPC grouping and body size, suggesting that individuals from one of the groups were significantly smaller than the other. These results give insight into the non-random nature of settlement in a species with protracted pelagic larval duration and could suggest the existence of chaotic genetic patchiness in J. edwardsii adult populations.