Norway spruce somatic embryos (SEs) exhibit extensive morphological and genotypic variation, and some cell lines are unable to complete the maturation stage of somatic embryogenesis. Two distinct types of clonal lines were identified based on their ability to undergo maturation: A-lines, which form mature SEs, and F-lines, which are unable to produce mature SEs. The cell division is altered and SE development was aborted in the F-lines as compared with the A-lines. Optimization of maturation medium by varying ABA, PEG and gellan gum concentration increased the yield of A-line SE production, but showed insignificant improvement in F-line SE production. Pre-treating PEMs in liquid medium containing ABA for 24 h prior to maturation induced mature SE formation in F-lines at a very low level. The F-lines contained significantly less free ABA than that of the A-lines, suggesting that the F-lines may lack the ability to uptake exogenous ABA or may quickly metabolize this ABA. The compromised maturation capacity in the F-line is associated with reduced expression of the early embryogenesis genes, e.g. KNOX (KNOTTED1–like homeobox), EF1-α (translation elongation factor 1- α) and VP1 (VIVIPAROUS 1), and with an inability to express ABA-mediated late embryogenesis genes, e.g., LEA (Late Embryogenesis Abundant) and SSP-2 (2S seed storage protein). An increase in the expression of these genes in the A-lines corresponds to the ability of the proembryogenic masses to successfully undergo maturation, producing mature SEs and normal trees. Results suggest that it is possible to increase A-line maturation frequency by altering media composition, but F-lines may be recalcitrant to maturation.