The pod-setting traits of 59 mustard (Brassica juncea) varieties including 30 cytoplasmic male sterile lines and 29 maintenance lines were studied with field investigation,molecular markers and cytological observation. The results of molecular markers analysis showed that 23 lines were hau cytoplasmic male sterile lines and 7 lines were ogu cytoplasmic male sterile lines. The results of cytological observation showed that siliques of the 29 maintainers,7 ogu cytoplasmic male sterile lines and 5 hau cytoplasmic male sterile lines were plump and vertical,while siliques of the 18 hau cytoplasmic male sterile lines were abnormal to different degree. Using the maintainer material with normal pod setting as the control (CK),the anther abortion and floral organ development of the mustard ogu cytoplasmic male sterile lines and the mustard hau cytoplasmic male sterile lines were cytologically observed. The results showed that the flower abortion of ogu cytoplasmic male sterile lines and hau cytoplasmic male sterile lines (normal pods) was the tapetum degraded in advance,while that of hau cytoplasmic male sterile lines (abnormal pods) was the formation of stamen-pistil chimera. It is indicated that the cytological formation mechanism of the pod-setting traits in cytoplasmic male sterile lines of mustard is preliminarily explored.