The endosperm is the storage tissue of seeds and is an important source of nutrients for humans and animals. In the previous work, the gene expression was characterized at 3 and 24 h after pollination (AP). The results suggested that eATP would act as a signalling molecule at the beginning of endosperm development and that sucrose metabolism could be related to EBN insensitivity. In addition, differentially expressed transcripts derived fragments (DETDFs) were related to the failure of fusion of the polar nuclei and the accumulation of storage products in seeds of Arabidopsis thaliana. The objective of the present study was to identify genes related to endosperm development in apomictic and sexual ovaries of Paspalum notatum 48 h AP, a stage at which development is prior to post-zygotic collapse. The cDNA-AFLP analysis was carried out to analyse different crosses and DETDFs categorized according to their function. The main cellular functions at 48 h AP were metabolism and signal transduction. Fourteen out of 39 DETDFs with relevant functional information were found in crosses for which normal endosperm development was expected. Three DETDFs were found in crosses where viable and unviable seeds were predicted and presented similarity with a casein kinase II (CK2), an enzyme that governs the accumulation of storage proteins in seeds of A. thaliana and Zea mays. The results obtained at 3, 24 and 48 h AP suggest that CK2 is involved in early endosperm development in P. notatum.