The SnRK1 complex, a metabolic regulator of nutrient deficit in plants, consists of a catalytic α -subunit and two regulatory subunits, β and γ that exist as several isoforms. To obtain insight into the developmental and stress conditions that regulate the expression of these regulatory subunits, four β subunits MtAKIN β 1- β 4, and three γ subunits MtAKIN βγ , MtSNF4β and MtAKIN γ were identified and characterized in seeds of M. truncatula . Their transcripts were found to accumulate differentially in vegetative and seed tissues and appear to be differentially modulated during germination and the imposition of stress. MtAKIN γ and MtAKIN β 3 showed identical patterns of expression upon osmotic shock, whereas transcripts of MtAKIN γ and MtAKIN β 1 were strongly up-regulated upon starvation of the radicles. Addition of glucose during the starvation process reversed this effect. MtAKIN β 2 and MtSNF4b were specifically induced upon the re-induction of desiccation tolerance in germinated, desiccation-sensitive radicles, whereas only MtSNF4b expression was repressed by an inhibitor of abscisic acid synthesis. A second γ subunit, MtAKIN βγ , was transiently expressed early during the induction of desiccation tolerance, and its expression could be modulated by blocking the respiratory ATP production by cyanide. The transcriptional regulation of the subunit isoforms showing identical expression profiles in germinating seeds appears to be under the control of different factors.