The Yersinia type III secretion system (T3SS) is environmentally responsive to enable its rapid induction upon contact with host cells and is necessary for Yersiniae to establish a replicative niche and cause disease. YopD, a translocator protein, represses the expression of T3SS genes until signalled by environmental cues, a mechanism known as the low calcium response. In this work, we investigated recognition of target genes by Yersinia pestis YopD. Expression of all genes of the T3SS was induced in a yopD mutant, though not to the same degree, with effector Yops most affected. Two, short AU-rich sequence elements up- and downstream of start codons of target genes were necessary but not sufficient for YopD mediated repression. Purified YopD–LcrH bound specifically to target RNAs in vitro with different relative affinities, with effector Yops having greater affinity. Together, the data suggest YopD binds to T3SS transcripts where it may prevent ribosome binding causing accelerated mRNA degradation. This regulatory mechanism may ensure an expression hierarchy during the low calcium response as low affinity YopD targets such as chaperones would be translated prior to high affinity targets such as effector Yops allowing the bacteria another layer of control over Yop translocation during infection.