Spermidine synthase (SpdS) is an aminopropyltransferase that transfers an aminopropyl moiety from decarboxylated S-adenosylmethionine to a variety of polyamines. SpdS enzymes convert putrescine to spermidine and its byproduct methylthioadenosine. In this study, we have overexpressed an N-terminal His₆-tagged SpdS from the fungal species Kluyveromyces lactis; it was overexpressed, purified and crystallized to obtain X-ray diffraction data at a high resolution of 1.9 Å. The K. lactis SpdS crystal belongs to the space group P2₁2₁2₁ with the following unit cell parameters: a = 65.252 Å, b = 98.180 Å, c = 102.134 Å, and α = β = γ = 90°. There are two molecules in the asymmetric unit.