If you only wanted RefSeq genomes (as annotated by NCBI) then there are 1542 Eukaryotic ones as of today (total number of Eukaryotic genomes is over 27K+).

https://www.ncbi.nlm.nih.gov/data-hub/genome/?taxon=2759&reference_only=true&annotated_only=true&refseq_annotation=true

If you are able to define a specific "taxID" group that you are interested in then the list above can be further refined.

You can use the NCBI datasets tool to download sequence: https://www.ncbi.nlm.nih.gov/datasets/ (an example shown in --> Automated way to pull representative/RefSeq genome using full species name? )

Then there are tools like genome_updater and ncbi-genome-download if you have accession numbers available.