The male gametophyte of the semi-aquatic fern, Marsilea vestita, produces multiciliated spermatozoids in a rapid developmental sequence that is controlled post-transcriptionally when dry microspores are placed in water. Development can be divided into two phases, mitosis and differentiation. During the mitotic phase, a series of nine successive division cycles produce 7 sterile cells and 32 spermatids in 4.5-5 h. During the next 5-6 h, each spermatid differentiates into a corkscrew-shaped motile spermatozoid with ∼140 cilia. In order to study the mechanisms that regulate spermatogenesis, we used RNAseq to generate a reference transcriptome that allowed us to assess abundance of transcripts at different stages of development. Here, we characterize transcripts present in the kinesin motor family. Over 120 kinesin-like sequences were identified in our transcriptome that represent 56 unique kinesin transcripts. Members of the kinesin-2, -4, -5, -7, -8, -9, -12, -13, and -14 families, in addition to several plant specific and 'orphan' kinesins are present. Most (91%) of these kinesin transcripts change in abundance throughout gametophyte development, with 52% of kinesin mRNAs enriched during the mitotic phase and 39% enriched during differentiation. Functional analyses of six kinesins with different patterns of transcript abundance show that the temporal regulation of these transcripts during gametogenesis correlates directly with kinesin protein function.